http://compbio.biosci.uq.edu.au/mediawiki/api.php?action=feedcontributions&user=PramodNair&feedformat=atomMDWiki - User contributions [en]2024-03-29T13:30:20ZUser contributionsMediaWiki 1.39.6http://compbio.biosci.uq.edu.au/mediawiki/index.php?title=PeopleMark&diff=16129PeopleMark2013-01-29T03:05:13Z<p>PramodNair: /* People */</p>
<hr />
<div>== People ==<br />
'''Principle Investigator'''<br />
<br />
[http://scmb.uq.edu.au/staff/alan-mark Prof. Alan Mark]<br />
<br />
[[Alan and his model plane]] <br />
<br />
'''Postdoctoral Fellows'''<br />
<br />
*[[Dr. Alpesh Malde]]<br />
*[http://compbio.biosci.uq.edu.au/~david/ Dr. David Poger]<br />
*[[Dr. Megan O'Mara]]<br />
<br />
'''Postgraduate Students'''<br />
<br />
*[[Zhi Guang Jia]] (PhD student)<br />
*[[Lachlan Casey]] (PhD student)<br />
<br />
'''Research Assistants'''<br />
<br />
<br />
''' Administration '''<br />
<br />
*[[Evelyn Smart]]<br />
<br />
'''Former Members'''<br />
*[[Matthew Breeze]]<br />
*[[Ying Xue]]<br />
*[[Dr. Itamar Kass]]<br />
*[[Dr. Maria Ratajczak]]<br />
*[[Ajinkya Joshi]]<br />
*[[Dr. Roy Zuo]]<br />
*[[Dr. Moritz Winger]]<br />
*[[Rong Chen]]<br />
*[[Pramod Nair]]</div>PramodNairhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Pramod_Nair&diff=16085Pramod Nair2012-06-21T12:37:42Z<p>PramodNair: /* Publications */</p>
<hr />
<div>Automated Force Field Topology Builder (ATB) for GROMOS and GROMACS : MD group of Prof. Alan E. Mark<br />
http://compbio.biosci.uq.edu.au/atb/ <br />
<br />
== Research Interests ==<br />
Computer Aided Drug Design (CADD) and Free Energy Calculations<br />
<br />
Alternate Free energy methods to aid high-throughput virtual screening in drug discovery<br />
<br />
Molecular Dynamics simulations of macromolecular and small molecular systems<br />
<br />
== Academic ==<br />
'''B. Pharm.''' Bombay College of Pharmacy, University of Mumbai, India 2001-2005 <br><br />
'''MS (Pharm.)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2005-2007 <br><br />
'''Junior Research Fellow (JRF)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2007-2008 <br><br />
'''PhD Student''' Molecular Dynamics Group, School of Chemistry and Molecular Biosciences (SCMB),University of Queensland, Australia 2009 <br><br />
<br />
== Publications ==<br />
1.'''Nair PC''', Malde AK, Drinkwater N, Mark AE. Missing Fragments: Detecting cooperative binding in fragment based drug design. ''ACS Medicinal Chemistry Letters'' 2012, Apr;3(4):322–326. [http://dx.doi.org/10.1021/ml300015u DOI: 10.1021/ml300015u]<br />
[http://www.rcsb.org/pdb/explore/explore.do?structureId=4DM3 PDBcode 4DM3]<br />
<br />
2. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, '''Nair PC''', Oostenbrink C, Mark AE. An Automated force field Topology Builder (ATB) and repository: version 1.0. ''Journal of Chemical Theory and Computation'' 2011, Oct;7(12):4026–4037.[http://dx.doi.org/10.1021/ct200196m DOI: 10.1021/ct200196m]<br />
<br />
3. Riniker S, Christ CD, Hansen N, Mark AE, '''Nair PC''', van Gunsteren WF. Comparison of Enveloping Distribution Sampling and Thermodynamic Integration to Calculate Binding Free Energies of Phenylethanolamine N-Methyltransferase Inhibitors. ''Journal of Chemical Physics'' 2011 Jul;135(2):024105-13. [http://dx.doi.org/10.1063/1.3604534 DOI:10.1063/1.3604534]<br />
<br />
4.'''Nair PC''', Malde AK, Mark AE."Using theory to reconcile experiment: the structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-MethylTransferase (PNMT)". ''Journal of Chemical Theory and Computation'' 2011, May;7(5):1458-1468. [http://dx.doi.org/10.1021/ct1007229 DOI: 10.1021/ct1007229]<br />
<br />
5.'''Nair PC'''. "Molecular Field Analysis (MFA) and other QSAR techniques in development of phosphatase inhibitors".<br />
''Anti-Cancer Agents in Medicinal Chemistry'' 2011 Jan;11(1):151-163. (Invited Review Article) [http://dx.doi.org/10.2174/187152011794941181 DOI: 10.2174/187152011794941181]<br />
<br />
6.'''Nair PC''', Sobhia ME. "Fingerprint directed scaffold hopping for identification of CCR2 antagonists".<br />
''Journal of Chemical Information and Modeling'' 2008 Sep;48(9):1891-902. [http://dx.doi.org/10.1021/ci800157j DOI: 10.1021/ci800157j]<br />
<br />
7.'''Nair PC''', Srikanth K, Sobhia ME. "QSAR studies on CCR2 antagonists with chiral sensitive hologram descriptors".<br />
''Bioorganic & Medicinal Chemistry Letters'' 2008 Feb;18(4):1323-30. [http://dx.doi.org/10.1016/j.bmcl.2008.01.023 DOI: 10.1016/j.bmcl.2008.01.023]<br />
<br />
8.Srikanth K, '''Nair PC''', Sobhia ME. "Probing the structural and topological requirements for CCR2 antagonism: holographic QSAR for <br> indolopiperidine derivatives".''Bioorganic & Medicinal Chemistry Letters'' 2008 Feb;18(4):1450-6. [http://dx.doi.org/10.1016/j.bmcl.2007.12.072 DOI: 10.1016/j.bmcl.2007.12.072]<br />
<br />
9.'''Nair PC''', Sobhia ME. "Comparative QSTR studies for predicting mutagenicity of nitro compounds".<br />
''Journal of Molecular Graphics and Modelling'' 2008 Feb;26(6):916-34. [http://dx.doi.org/10.1016/j.jmgm.2007.06.006 DOI:10.1016/j.jmgm.2007.06.006]<br />
<br />
10.'''Nair PC''', Sobhia ME. "Quantitative structure activity relationship studies on thiourea analogues as influenza virus neuraminidase inhibitors". ''European Journal of Medicinal Chemistry'' 2008 Feb;43(2):293-9. [http://dx.doi.org/10.1016/j.ejmech.2007.03.020 DOI: 10.1016/j.ejmech.2007.03.020]<br />
<br />
11.'''Nair PC''', Sobhia ME."CoMFA based de novo design of pyridazine analogs as PTP1B inhibitors".<br />
''Journal of Molecular Graphics and Modelling'' 2007 Jul;26(1):117-23. [http://dx.doi.org/10.1016/j.jmgm.2006.10.002 DOI: 10.1016/j.jmgm.2006.10.002]<br />
<br />
12.Khurana J, '''Nair P''',Sobhia ME. "Design of Allosteric Ligands Using Computer Aided Drug Design (CADD) Techniques", Current Research & Information on Pharmaceutical Sciences (CRIPS), 2006 Apr;7(2):8-13.(Review Article)<br><br />
<br />
== Poster Presentations ==<br />
1.'''Nair PC''', Malde AK, Mark AE."Validation of fragment hits in X-ray crystal complexes", The East Coast Protein Meeting, Coffs Harbour NSW, Australia, 15-17th July 2011<br />
<br />
2.'''Nair PC''', Malde AK, Mark AE."The structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-methyltransferase (PNMT): A Molecular Dynamics and Free Energy study", Molecular Modelling 2010, Melbourne, Australia, 28Nov-1Dec 2010.<br />
<br />
3.'''Nair PC''', Malde AK, Mark AE.Investigating structural requirements for PNMT inhibition: A molecular dynamics and free energy calculation study", Division of chemistry and structural biology symposium, Institute of Molecular Bioscience, Brisbane, Australia, Nov 18-19 2010.<br />
<br />
4.'''Nair PC''', Malde AK, Mark AE. "Investigation of ligand interaction and binding free Energy of 1,2,3,4 tetrahydroisoquinoline analogues as PNMT inhibitors", 61st Indian Pharmaceutical Congress, 11-13 December 2009.<br />
<br />
5.'''Nair PC''', Sobhia ME. "Identification of Novel CCR2 Scaffolds Through Fingerprint Directed Virtual Screening", Virtual Discovery Europe (Computer Aided Drug Design and Screening) London, England, 24-25 October 2007. (Presented by Dr. M. Elizabeth Sobhia, NIPER )<br />
<br />
6.'''Nair PC''', Sobhia ME. "Synergistic application of target structure based alignment and 3D-QSAR study of protein tyrosine phosphatases 1B (PTP1B) inhibitors", Workshop on Pharmcoinformatics: Tools for Drug Target Identification, NIPER, India, March 14-16, 2007.<br />
<br />
7.'''Nair PC''', Sobhia ME. "Quantitative Structure Toxicity Relationship (QSTR) Studies for Predicting Mutagenicity of Nitro Compounds", International Conference on Chemoinformatics, NCL, Pune, India, Jan 22, 2007.<br />
<br />
8.'''Nair PC''', Sobhia ME. "Design of novel PTP1B inhibitors using 3D-QSAR and concept of hypothetical cavity generation", Workshop on Pharmacoinformatics: QSAR, NIPER, India, March 3-4, 2006.<br />
<br />
== Other Conferences/Scientific visits ==<br />
<br />
Structural Biology Symposium, Institute for Glycomics, Griffith University, Gold Coast, Australia, 2009. <br />
<br />
Molecular Modelling (MM2009), Gold Coast, Queensland, Australia, July 26-29 2009. <br />
<br />
Attended 8th National Center of Competence in Research (NCCR) Practical Course in the area of computational structural biology, Kandersteg, Switzerland, Jan 10-15 2010.<br />
<br />
Visited as a scientific guest in the laboratory of Prof. Wilfred F. van Gunsteren, ETH Zurich, Switzerland, Jan 16-29 2010.<br />
<br />
== Contact Details ==<br />
<br />
Endeavour IPRS Doctoral Fellow <br><br />
Molecular Dynamics Group <br><br />
School of Chemistry and Molecular Biosciences (SCMB) <br><br />
Molecular Biosciences Building (#76) <br><br />
The University of Queensland <br><br />
St. Lucia Campus, Brisbane, QLD 4072 <br><br />
Australia <br><br />
<br />
'''email''' p.nair@uq.edu.au</div>PramodNairhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Pramod_Nair&diff=16066Pramod Nair2012-04-27T06:20:12Z<p>PramodNair: /* Publications */</p>
<hr />
<div>Automated Force Field Topology Builder (ATB) for GROMOS and GROMACS : MD group of Prof. Alan E. Mark<br />
http://compbio.biosci.uq.edu.au/atb/ <br />
<br />
== Research Interests ==<br />
Computer Aided Drug Design (CADD) and Free Energy Calculations<br />
<br />
Alternate Free energy methods to aid high-throughput virtual screening in drug discovery<br />
<br />
Molecular Dynamics simulations of macromolecular and small molecular systems<br />
<br />
== Academic ==<br />
'''B. Pharm.''' Bombay College of Pharmacy, University of Mumbai, India 2001-2005 <br><br />
'''MS (Pharm.)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2005-2007 <br><br />
'''Junior Research Fellow (JRF)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2007-2008 <br><br />
'''PhD Student''' Molecular Dynamics Group, School of Chemistry and Molecular Biosciences (SCMB),University of Queensland, Australia 2009 <br><br />
<br />
== Publications ==<br />
1.'''Nair PC''', Malde AK, Drinkwater N, Mark AE. Missing Fragments: Detecting cooperative binding in fragment based drug design. ''ACS Med. Chem. Lett.'' 2012, Apr;3(4):322–326. [http://dx.doi.org/10.1021/ml300015u DOI: 10.1021/ml300015u]<br />
[http://www.rcsb.org/pdb/explore/explore.do?structureId=4DM3 PDBcode 4DM3]<br />
<br />
2. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, '''Nair PC''', Oostenbrink C, Mark AE. An Automated force field Topology Builder (ATB) and repository: version 1.0. ''J Chem Theory Comput.'' 2011, Oct;7(12):4026–4037.[http://dx.doi.org/10.1021/ct200196m DOI: 10.1021/ct200196m]<br />
<br />
3. Riniker S, Christ CD, Hansen N, Mark AE, '''Nair PC''', van Gunsteren WF. Comparison of Enveloping Distribution Sampling and Thermodynamic Integration to Calculate Binding Free Energies of Phenylethanolamine N-Methyltransferase Inhibitors. ''J Chem Phys.'' 2011 Jul;135(2):024105-13. [http://dx.doi.org/10.1063/1.3604534 DOI:10.1063/1.3604534]<br />
<br />
4.'''Nair PC''', Malde AK, Mark AE."Using theory to reconcile experiment: the structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-MethylTransferase (PNMT)". ''J Chem Theory Comput.'' 2011, May;7(5):1458-1468. [http://dx.doi.org/10.1021/ct1007229 DOI: 10.1021/ct1007229]<br />
<br />
5.'''Nair PC'''. "Molecular Field Analysis (MFA) and other QSAR techniques in development of phosphatase inhibitors".<br />
''Anticancer Agents Med Chem.'' 2011 Jan;11(1):151-163. (Invited Review Article) [http://dx.doi.org/10.2174/187152011794941181 DOI: 10.2174/187152011794941181]<br />
<br />
6.'''Nair PC''', Sobhia ME. "Fingerprint directed scaffold hopping for identification of CCR2 antagonists".<br />
''J Chem Inf Model.'' 2008 Sep;48(9):1891-902. [http://dx.doi.org/10.1021/ci800157j DOI: 10.1021/ci800157j]<br />
<br />
7.'''Nair PC''', Srikanth K, Sobhia ME. "QSAR studies on CCR2 antagonists with chiral sensitive hologram descriptors".<br />
''Bioorg Med Chem Lett.'' 2008 Feb;18(4):1323-30. [http://dx.doi.org/10.1016/j.bmcl.2008.01.023 DOI: 10.1016/j.bmcl.2008.01.023]<br />
<br />
8.Srikanth K, '''Nair PC''', Sobhia ME. "Probing the structural and topological requirements for CCR2 antagonism: holographic QSAR for <br> indolopiperidine derivatives".''Bioorg Med Chem Lett.'' 2008 Feb;18(4):1450-6. [http://dx.doi.org/10.1016/j.bmcl.2007.12.072 DOI: 10.1016/j.bmcl.2007.12.072]<br />
<br />
9.'''Nair PC''', Sobhia ME. "Comparative QSTR studies for predicting mutagenicity of nitro compounds".<br />
''J Mol Graph Model.'' 2008 Feb;26(6):916-34. [http://dx.doi.org/10.1016/j.jmgm.2007.06.006 DOI:10.1016/j.jmgm.2007.06.006]<br />
<br />
10.'''Nair PC''', Sobhia ME. "Quantitative structure activity relationship studies on thiourea analogues as influenza virus neuraminidase inhibitors". ''Eur J Med Chem.'' 2008 Feb;43(2):293-9. [http://dx.doi.org/10.1016/j.ejmech.2007.03.020 DOI: 10.1016/j.ejmech.2007.03.020]<br />
<br />
11.'''Nair PC''', Sobhia ME."CoMFA based de novo design of pyridazine analogs as PTP1B inhibitors".<br />
''J Mol Graph Model.'' 2007 Jul;26(1):117-23. [http://dx.doi.org/10.1016/j.jmgm.2006.10.002 DOI: 10.1016/j.jmgm.2006.10.002]<br />
<br />
12.Khurana J, '''Nair P''',Sobhia ME. "Design of Allosteric Ligands Using Computer Aided Drug Design (CADD) Techniques", Current Research & Information on Pharmaceutical Sciences (CRIPS), 2006 Apr;7(2):8-13.(Review Article)<br><br />
<br />
== Poster Presentations ==<br />
1.'''Nair PC''', Malde AK, Mark AE."Validation of fragment hits in X-ray crystal complexes", The East Coast Protein Meeting, Coffs Harbour NSW, Australia, 15-17th July 2011<br />
<br />
2.'''Nair PC''', Malde AK, Mark AE."The structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-methyltransferase (PNMT): A Molecular Dynamics and Free Energy study", Molecular Modelling 2010, Melbourne, Australia, 28Nov-1Dec 2010.<br />
<br />
3.'''Nair PC''', Malde AK, Mark AE.Investigating structural requirements for PNMT inhibition: A molecular dynamics and free energy calculation study", Division of chemistry and structural biology symposium, Institute of Molecular Bioscience, Brisbane, Australia, Nov 18-19 2010.<br />
<br />
4.'''Nair PC''', Malde AK, Mark AE. "Investigation of ligand interaction and binding free Energy of 1,2,3,4 tetrahydroisoquinoline analogues as PNMT inhibitors", 61st Indian Pharmaceutical Congress, 11-13 December 2009.<br />
<br />
5.'''Nair PC''', Sobhia ME. "Identification of Novel CCR2 Scaffolds Through Fingerprint Directed Virtual Screening", Virtual Discovery Europe (Computer Aided Drug Design and Screening) London, England, 24-25 October 2007. (Presented by Dr. M. Elizabeth Sobhia, NIPER )<br />
<br />
6.'''Nair PC''', Sobhia ME. "Synergistic application of target structure based alignment and 3D-QSAR study of protein tyrosine phosphatases 1B (PTP1B) inhibitors", Workshop on Pharmcoinformatics: Tools for Drug Target Identification, NIPER, India, March 14-16, 2007.<br />
<br />
7.'''Nair PC''', Sobhia ME. "Quantitative Structure Toxicity Relationship (QSTR) Studies for Predicting Mutagenicity of Nitro Compounds", International Conference on Chemoinformatics, NCL, Pune, India, Jan 22, 2007.<br />
<br />
8.'''Nair PC''', Sobhia ME. "Design of novel PTP1B inhibitors using 3D-QSAR and concept of hypothetical cavity generation", Workshop on Pharmacoinformatics: QSAR, NIPER, India, March 3-4, 2006.<br />
<br />
== Other Conferences/Scientific visits ==<br />
<br />
Structural Biology Symposium, Institute for Glycomics, Griffith University, Gold Coast, Australia, 2009. <br />
<br />
Molecular Modelling (MM2009), Gold Coast, Queensland, Australia, July 26-29 2009. <br />
<br />
Attended 8th National Center of Competence in Research (NCCR) Practical Course in the area of computational structural biology, Kandersteg, Switzerland, Jan 10-15 2010.<br />
<br />
Visited as a scientific guest in the laboratory of Prof. Wilfred F. van Gunsteren, ETH Zurich, Switzerland, Jan 16-29 2010.<br />
<br />
== Contact Details ==<br />
<br />
Endeavour IPRS Doctoral Fellow <br><br />
Molecular Dynamics Group <br><br />
School of Chemistry and Molecular Biosciences (SCMB) <br><br />
Molecular Biosciences Building (#76) <br><br />
The University of Queensland <br><br />
St. Lucia Campus, Brisbane, QLD 4072 <br><br />
Australia <br><br />
<br />
'''email''' p.nair@uq.edu.au</div>PramodNairhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Pramod_Nair&diff=16065Pramod Nair2012-04-27T06:19:55Z<p>PramodNair: /* Publications */</p>
<hr />
<div>Automated Force Field Topology Builder (ATB) for GROMOS and GROMACS : MD group of Prof. Alan E. Mark<br />
http://compbio.biosci.uq.edu.au/atb/ <br />
<br />
== Research Interests ==<br />
Computer Aided Drug Design (CADD) and Free Energy Calculations<br />
<br />
Alternate Free energy methods to aid high-throughput virtual screening in drug discovery<br />
<br />
Molecular Dynamics simulations of macromolecular and small molecular systems<br />
<br />
== Academic ==<br />
'''B. Pharm.''' Bombay College of Pharmacy, University of Mumbai, India 2001-2005 <br><br />
'''MS (Pharm.)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2005-2007 <br><br />
'''Junior Research Fellow (JRF)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2007-2008 <br><br />
'''PhD Student''' Molecular Dynamics Group, School of Chemistry and Molecular Biosciences (SCMB),University of Queensland, Australia 2009 <br><br />
<br />
== Publications ==<br />
1.'''Nair PC''', Malde AK, Drinkwater N, Mark AE. Missing Fragments: Detecting cooperative binding in fragment based drug design. ''ACS Med. Chem. Lett.'' 2012, Apr;3(4):322–326. <br />
[http://dx.doi.org/10.1021/ml300015u DOI: 10.1021/ml300015u]<br />
[http://www.rcsb.org/pdb/explore/explore.do?structureId=4DM3 PDBcode 4DM3]<br />
<br />
2. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, '''Nair PC''', Oostenbrink C, Mark AE. An Automated force field Topology Builder (ATB) and repository: version 1.0. ''J Chem Theory Comput.'' 2011, Oct;7(12):4026–4037.[http://dx.doi.org/10.1021/ct200196m DOI: 10.1021/ct200196m]<br />
<br />
3. Riniker S, Christ CD, Hansen N, Mark AE, '''Nair PC''', van Gunsteren WF. Comparison of Enveloping Distribution Sampling and Thermodynamic Integration to Calculate Binding Free Energies of Phenylethanolamine N-Methyltransferase Inhibitors. ''J Chem Phys.'' 2011 Jul;135(2):024105-13. [http://dx.doi.org/10.1063/1.3604534 DOI:10.1063/1.3604534]<br />
<br />
4.'''Nair PC''', Malde AK, Mark AE."Using theory to reconcile experiment: the structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-MethylTransferase (PNMT)". ''J Chem Theory Comput.'' 2011, May;7(5):1458-1468. [http://dx.doi.org/10.1021/ct1007229 DOI: 10.1021/ct1007229]<br />
<br />
5.'''Nair PC'''. "Molecular Field Analysis (MFA) and other QSAR techniques in development of phosphatase inhibitors".<br />
''Anticancer Agents Med Chem.'' 2011 Jan;11(1):151-163. (Invited Review Article) [http://dx.doi.org/10.2174/187152011794941181 DOI: 10.2174/187152011794941181]<br />
<br />
6.'''Nair PC''', Sobhia ME. "Fingerprint directed scaffold hopping for identification of CCR2 antagonists".<br />
''J Chem Inf Model.'' 2008 Sep;48(9):1891-902. [http://dx.doi.org/10.1021/ci800157j DOI: 10.1021/ci800157j]<br />
<br />
7.'''Nair PC''', Srikanth K, Sobhia ME. "QSAR studies on CCR2 antagonists with chiral sensitive hologram descriptors".<br />
''Bioorg Med Chem Lett.'' 2008 Feb;18(4):1323-30. [http://dx.doi.org/10.1016/j.bmcl.2008.01.023 DOI: 10.1016/j.bmcl.2008.01.023]<br />
<br />
8.Srikanth K, '''Nair PC''', Sobhia ME. "Probing the structural and topological requirements for CCR2 antagonism: holographic QSAR for <br> indolopiperidine derivatives".''Bioorg Med Chem Lett.'' 2008 Feb;18(4):1450-6. [http://dx.doi.org/10.1016/j.bmcl.2007.12.072 DOI: 10.1016/j.bmcl.2007.12.072]<br />
<br />
9.'''Nair PC''', Sobhia ME. "Comparative QSTR studies for predicting mutagenicity of nitro compounds".<br />
''J Mol Graph Model.'' 2008 Feb;26(6):916-34. [http://dx.doi.org/10.1016/j.jmgm.2007.06.006 DOI:10.1016/j.jmgm.2007.06.006]<br />
<br />
10.'''Nair PC''', Sobhia ME. "Quantitative structure activity relationship studies on thiourea analogues as influenza virus neuraminidase inhibitors". ''Eur J Med Chem.'' 2008 Feb;43(2):293-9. [http://dx.doi.org/10.1016/j.ejmech.2007.03.020 DOI: 10.1016/j.ejmech.2007.03.020]<br />
<br />
11.'''Nair PC''', Sobhia ME."CoMFA based de novo design of pyridazine analogs as PTP1B inhibitors".<br />
''J Mol Graph Model.'' 2007 Jul;26(1):117-23. [http://dx.doi.org/10.1016/j.jmgm.2006.10.002 DOI: 10.1016/j.jmgm.2006.10.002]<br />
<br />
12.Khurana J, '''Nair P''',Sobhia ME. "Design of Allosteric Ligands Using Computer Aided Drug Design (CADD) Techniques", Current Research & Information on Pharmaceutical Sciences (CRIPS), 2006 Apr;7(2):8-13.(Review Article)<br><br />
<br />
== Poster Presentations ==<br />
1.'''Nair PC''', Malde AK, Mark AE."Validation of fragment hits in X-ray crystal complexes", The East Coast Protein Meeting, Coffs Harbour NSW, Australia, 15-17th July 2011<br />
<br />
2.'''Nair PC''', Malde AK, Mark AE."The structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-methyltransferase (PNMT): A Molecular Dynamics and Free Energy study", Molecular Modelling 2010, Melbourne, Australia, 28Nov-1Dec 2010.<br />
<br />
3.'''Nair PC''', Malde AK, Mark AE.Investigating structural requirements for PNMT inhibition: A molecular dynamics and free energy calculation study", Division of chemistry and structural biology symposium, Institute of Molecular Bioscience, Brisbane, Australia, Nov 18-19 2010.<br />
<br />
4.'''Nair PC''', Malde AK, Mark AE. "Investigation of ligand interaction and binding free Energy of 1,2,3,4 tetrahydroisoquinoline analogues as PNMT inhibitors", 61st Indian Pharmaceutical Congress, 11-13 December 2009.<br />
<br />
5.'''Nair PC''', Sobhia ME. "Identification of Novel CCR2 Scaffolds Through Fingerprint Directed Virtual Screening", Virtual Discovery Europe (Computer Aided Drug Design and Screening) London, England, 24-25 October 2007. (Presented by Dr. M. Elizabeth Sobhia, NIPER )<br />
<br />
6.'''Nair PC''', Sobhia ME. "Synergistic application of target structure based alignment and 3D-QSAR study of protein tyrosine phosphatases 1B (PTP1B) inhibitors", Workshop on Pharmcoinformatics: Tools for Drug Target Identification, NIPER, India, March 14-16, 2007.<br />
<br />
7.'''Nair PC''', Sobhia ME. "Quantitative Structure Toxicity Relationship (QSTR) Studies for Predicting Mutagenicity of Nitro Compounds", International Conference on Chemoinformatics, NCL, Pune, India, Jan 22, 2007.<br />
<br />
8.'''Nair PC''', Sobhia ME. "Design of novel PTP1B inhibitors using 3D-QSAR and concept of hypothetical cavity generation", Workshop on Pharmacoinformatics: QSAR, NIPER, India, March 3-4, 2006.<br />
<br />
== Other Conferences/Scientific visits ==<br />
<br />
Structural Biology Symposium, Institute for Glycomics, Griffith University, Gold Coast, Australia, 2009. <br />
<br />
Molecular Modelling (MM2009), Gold Coast, Queensland, Australia, July 26-29 2009. <br />
<br />
Attended 8th National Center of Competence in Research (NCCR) Practical Course in the area of computational structural biology, Kandersteg, Switzerland, Jan 10-15 2010.<br />
<br />
Visited as a scientific guest in the laboratory of Prof. Wilfred F. van Gunsteren, ETH Zurich, Switzerland, Jan 16-29 2010.<br />
<br />
== Contact Details ==<br />
<br />
Endeavour IPRS Doctoral Fellow <br><br />
Molecular Dynamics Group <br><br />
School of Chemistry and Molecular Biosciences (SCMB) <br><br />
Molecular Biosciences Building (#76) <br><br />
The University of Queensland <br><br />
St. Lucia Campus, Brisbane, QLD 4072 <br><br />
Australia <br><br />
<br />
'''email''' p.nair@uq.edu.au</div>PramodNairhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Pramod_Nair&diff=16064Pramod Nair2012-04-27T06:19:38Z<p>PramodNair: /* Publications */</p>
<hr />
<div>Automated Force Field Topology Builder (ATB) for GROMOS and GROMACS : MD group of Prof. Alan E. Mark<br />
http://compbio.biosci.uq.edu.au/atb/ <br />
<br />
== Research Interests ==<br />
Computer Aided Drug Design (CADD) and Free Energy Calculations<br />
<br />
Alternate Free energy methods to aid high-throughput virtual screening in drug discovery<br />
<br />
Molecular Dynamics simulations of macromolecular and small molecular systems<br />
<br />
== Academic ==<br />
'''B. Pharm.''' Bombay College of Pharmacy, University of Mumbai, India 2001-2005 <br><br />
'''MS (Pharm.)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2005-2007 <br><br />
'''Junior Research Fellow (JRF)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2007-2008 <br><br />
'''PhD Student''' Molecular Dynamics Group, School of Chemistry and Molecular Biosciences (SCMB),University of Queensland, Australia 2009 <br><br />
<br />
== Publications ==<br />
1.'''Nair PC''', Malde AK, Drinkwater N, Mark AE. Missing Fragments: Detecting cooperative binding in fragment based drug design. ''ACS Med. Chem. Lett.'' 2012, Apr;3(4):322–326. [http://dx.doi.org/10.1021/ml300015u DOI: 10.1021/ml300015u]<br />
[http://www.rcsb.org/pdb/explore/explore.do?structureId=4DM3 PDBcode 4DM3]<br />
<br />
2. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, '''Nair PC''', Oostenbrink C, Mark AE. An Automated force field Topology Builder (ATB) and repository: version 1.0. ''J Chem Theory Comput.'' 2011, Oct;7(12):4026–4037.[http://dx.doi.org/10.1021/ct200196m DOI: 10.1021/ct200196m]<br />
<br />
3. Riniker S, Christ CD, Hansen N, Mark AE, '''Nair PC''', van Gunsteren WF. Comparison of Enveloping Distribution Sampling and Thermodynamic Integration to Calculate Binding Free Energies of Phenylethanolamine N-Methyltransferase Inhibitors. ''J Chem Phys.'' 2011 Jul;135(2):024105-13. [http://dx.doi.org/10.1063/1.3604534 DOI:10.1063/1.3604534]<br />
<br />
4.'''Nair PC''', Malde AK, Mark AE."Using theory to reconcile experiment: the structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-MethylTransferase (PNMT)". ''J Chem Theory Comput.'' 2011, May;7(5):1458-1468. [http://dx.doi.org/10.1021/ct1007229 DOI: 10.1021/ct1007229]<br />
<br />
5.'''Nair PC'''. "Molecular Field Analysis (MFA) and other QSAR techniques in development of phosphatase inhibitors".<br />
''Anticancer Agents Med Chem.'' 2011 Jan;11(1):151-163. (Invited Review Article) [http://dx.doi.org/10.2174/187152011794941181 DOI: 10.2174/187152011794941181]<br />
<br />
6.'''Nair PC''', Sobhia ME. "Fingerprint directed scaffold hopping for identification of CCR2 antagonists".<br />
''J Chem Inf Model.'' 2008 Sep;48(9):1891-902. [http://dx.doi.org/10.1021/ci800157j DOI: 10.1021/ci800157j]<br />
<br />
7.'''Nair PC''', Srikanth K, Sobhia ME. "QSAR studies on CCR2 antagonists with chiral sensitive hologram descriptors".<br />
''Bioorg Med Chem Lett.'' 2008 Feb;18(4):1323-30. [http://dx.doi.org/10.1016/j.bmcl.2008.01.023 DOI: 10.1016/j.bmcl.2008.01.023]<br />
<br />
8.Srikanth K, '''Nair PC''', Sobhia ME. "Probing the structural and topological requirements for CCR2 antagonism: holographic QSAR for <br> indolopiperidine derivatives".''Bioorg Med Chem Lett.'' 2008 Feb;18(4):1450-6. [http://dx.doi.org/10.1016/j.bmcl.2007.12.072 DOI: 10.1016/j.bmcl.2007.12.072]<br />
<br />
9.'''Nair PC''', Sobhia ME. "Comparative QSTR studies for predicting mutagenicity of nitro compounds".<br />
''J Mol Graph Model.'' 2008 Feb;26(6):916-34. [http://dx.doi.org/10.1016/j.jmgm.2007.06.006 DOI:10.1016/j.jmgm.2007.06.006]<br />
<br />
10.'''Nair PC''', Sobhia ME. "Quantitative structure activity relationship studies on thiourea analogues as influenza virus neuraminidase inhibitors". ''Eur J Med Chem.'' 2008 Feb;43(2):293-9. [http://dx.doi.org/10.1016/j.ejmech.2007.03.020 DOI: 10.1016/j.ejmech.2007.03.020]<br />
<br />
11.'''Nair PC''', Sobhia ME."CoMFA based de novo design of pyridazine analogs as PTP1B inhibitors".<br />
''J Mol Graph Model.'' 2007 Jul;26(1):117-23. [http://dx.doi.org/10.1016/j.jmgm.2006.10.002 DOI: 10.1016/j.jmgm.2006.10.002]<br />
<br />
12.Khurana J, '''Nair P''',Sobhia ME. "Design of Allosteric Ligands Using Computer Aided Drug Design (CADD) Techniques", Current Research & Information on Pharmaceutical Sciences (CRIPS), 2006 Apr;7(2):8-13.(Review Article)<br><br />
<br />
== Poster Presentations ==<br />
1.'''Nair PC''', Malde AK, Mark AE."Validation of fragment hits in X-ray crystal complexes", The East Coast Protein Meeting, Coffs Harbour NSW, Australia, 15-17th July 2011<br />
<br />
2.'''Nair PC''', Malde AK, Mark AE."The structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-methyltransferase (PNMT): A Molecular Dynamics and Free Energy study", Molecular Modelling 2010, Melbourne, Australia, 28Nov-1Dec 2010.<br />
<br />
3.'''Nair PC''', Malde AK, Mark AE.Investigating structural requirements for PNMT inhibition: A molecular dynamics and free energy calculation study", Division of chemistry and structural biology symposium, Institute of Molecular Bioscience, Brisbane, Australia, Nov 18-19 2010.<br />
<br />
4.'''Nair PC''', Malde AK, Mark AE. "Investigation of ligand interaction and binding free Energy of 1,2,3,4 tetrahydroisoquinoline analogues as PNMT inhibitors", 61st Indian Pharmaceutical Congress, 11-13 December 2009.<br />
<br />
5.'''Nair PC''', Sobhia ME. "Identification of Novel CCR2 Scaffolds Through Fingerprint Directed Virtual Screening", Virtual Discovery Europe (Computer Aided Drug Design and Screening) London, England, 24-25 October 2007. (Presented by Dr. M. Elizabeth Sobhia, NIPER )<br />
<br />
6.'''Nair PC''', Sobhia ME. "Synergistic application of target structure based alignment and 3D-QSAR study of protein tyrosine phosphatases 1B (PTP1B) inhibitors", Workshop on Pharmcoinformatics: Tools for Drug Target Identification, NIPER, India, March 14-16, 2007.<br />
<br />
7.'''Nair PC''', Sobhia ME. "Quantitative Structure Toxicity Relationship (QSTR) Studies for Predicting Mutagenicity of Nitro Compounds", International Conference on Chemoinformatics, NCL, Pune, India, Jan 22, 2007.<br />
<br />
8.'''Nair PC''', Sobhia ME. "Design of novel PTP1B inhibitors using 3D-QSAR and concept of hypothetical cavity generation", Workshop on Pharmacoinformatics: QSAR, NIPER, India, March 3-4, 2006.<br />
<br />
== Other Conferences/Scientific visits ==<br />
<br />
Structural Biology Symposium, Institute for Glycomics, Griffith University, Gold Coast, Australia, 2009. <br />
<br />
Molecular Modelling (MM2009), Gold Coast, Queensland, Australia, July 26-29 2009. <br />
<br />
Attended 8th National Center of Competence in Research (NCCR) Practical Course in the area of computational structural biology, Kandersteg, Switzerland, Jan 10-15 2010.<br />
<br />
Visited as a scientific guest in the laboratory of Prof. Wilfred F. van Gunsteren, ETH Zurich, Switzerland, Jan 16-29 2010.<br />
<br />
== Contact Details ==<br />
<br />
Endeavour IPRS Doctoral Fellow <br><br />
Molecular Dynamics Group <br><br />
School of Chemistry and Molecular Biosciences (SCMB) <br><br />
Molecular Biosciences Building (#76) <br><br />
The University of Queensland <br><br />
St. Lucia Campus, Brisbane, QLD 4072 <br><br />
Australia <br><br />
<br />
'''email''' p.nair@uq.edu.au</div>PramodNairhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Pramod_Nair&diff=16058Pramod Nair2012-03-27T00:30:13Z<p>PramodNair: /* Publications */</p>
<hr />
<div>Automated Force Field Topology Builder (ATB) for GROMOS and GROMACS : MD group of Prof. Alan E. Mark<br />
http://compbio.biosci.uq.edu.au/atb/ <br />
<br />
== Research Interests ==<br />
Computer Aided Drug Design (CADD) and Free Energy Calculations<br />
<br />
Alternate Free energy methods to aid high-throughput virtual screening in drug discovery<br />
<br />
Molecular Dynamics simulations of macromolecular and small molecular systems<br />
<br />
== Academic ==<br />
'''B. Pharm.''' Bombay College of Pharmacy, University of Mumbai, India 2001-2005 <br><br />
'''MS (Pharm.)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2005-2007 <br><br />
'''Junior Research Fellow (JRF)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2007-2008 <br><br />
'''PhD Student''' Molecular Dynamics Group, School of Chemistry and Molecular Biosciences (SCMB),University of Queensland, Australia 2009 <br><br />
<br />
== Publications ==<br />
1.'''Nair PC''', Malde AK, Drinkwater N, Mark AE. Missing Fragments: Detecting cooperative binding in fragment based drug design. ''ACS Med. Chem. Lett.'' 2012, [http://dx.doi.org/10.1021/ml300015u DOI: 10.1021/ml300015u]<br />
[http://www.rcsb.org/pdb/explore/explore.do?structureId=4DM3 PDBcode 4DM3]<br />
<br />
2. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, '''Nair PC''', Oostenbrink C, Mark AE. An Automated force field Topology Builder (ATB) and repository: version 1.0. ''J Chem Theory Comput.'' 2011, Oct;7(12):4026–4037.[http://dx.doi.org/10.1021/ct200196m DOI: 10.1021/ct200196m]<br />
<br />
3. Riniker S, Christ CD, Hansen N, Mark AE, '''Nair PC''', van Gunsteren WF. Comparison of Enveloping Distribution Sampling and Thermodynamic Integration to Calculate Binding Free Energies of Phenylethanolamine N-Methyltransferase Inhibitors. ''J Chem Phys.'' 2011 Jul;135(2):024105-13. [http://dx.doi.org/10.1063/1.3604534 DOI:10.1063/1.3604534]<br />
<br />
4.'''Nair PC''', Malde AK, Mark AE."Using theory to reconcile experiment: the structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-MethylTransferase (PNMT)". ''J Chem Theory Comput.'' 2011, May;7(5):1458-1468. [http://dx.doi.org/10.1021/ct1007229 DOI: 10.1021/ct1007229]<br />
<br />
5.'''Nair PC'''. "Molecular Field Analysis (MFA) and other QSAR techniques in development of phosphatase inhibitors".<br />
''Anticancer Agents Med Chem.'' 2011 Jan;11(1):151-163. (Invited Review Article) [http://dx.doi.org/10.2174/187152011794941181 DOI: 10.2174/187152011794941181]<br />
<br />
6.'''Nair PC''', Sobhia ME. "Fingerprint directed scaffold hopping for identification of CCR2 antagonists".<br />
''J Chem Inf Model.'' 2008 Sep;48(9):1891-902. [http://dx.doi.org/10.1021/ci800157j DOI: 10.1021/ci800157j]<br />
<br />
7.'''Nair PC''', Srikanth K, Sobhia ME. "QSAR studies on CCR2 antagonists with chiral sensitive hologram descriptors".<br />
''Bioorg Med Chem Lett.'' 2008 Feb;18(4):1323-30. [http://dx.doi.org/10.1016/j.bmcl.2008.01.023 DOI: 10.1016/j.bmcl.2008.01.023]<br />
<br />
8.Srikanth K, '''Nair PC''', Sobhia ME. "Probing the structural and topological requirements for CCR2 antagonism: holographic QSAR for <br> indolopiperidine derivatives".''Bioorg Med Chem Lett.'' 2008 Feb;18(4):1450-6. [http://dx.doi.org/10.1016/j.bmcl.2007.12.072 DOI: 10.1016/j.bmcl.2007.12.072]<br />
<br />
9.'''Nair PC''', Sobhia ME. "Comparative QSTR studies for predicting mutagenicity of nitro compounds".<br />
''J Mol Graph Model.'' 2008 Feb;26(6):916-34. [http://dx.doi.org/10.1016/j.jmgm.2007.06.006 DOI:10.1016/j.jmgm.2007.06.006]<br />
<br />
10.'''Nair PC''', Sobhia ME. "Quantitative structure activity relationship studies on thiourea analogues as influenza virus neuraminidase inhibitors". ''Eur J Med Chem.'' 2008 Feb;43(2):293-9. [http://dx.doi.org/10.1016/j.ejmech.2007.03.020 DOI: 10.1016/j.ejmech.2007.03.020]<br />
<br />
11.'''Nair PC''', Sobhia ME."CoMFA based de novo design of pyridazine analogs as PTP1B inhibitors".<br />
''J Mol Graph Model.'' 2007 Jul;26(1):117-23. [http://dx.doi.org/10.1016/j.jmgm.2006.10.002 DOI: 10.1016/j.jmgm.2006.10.002]<br />
<br />
12.Khurana J, '''Nair P''',Sobhia ME. "Design of Allosteric Ligands Using Computer Aided Drug Design (CADD) Techniques", Current Research & Information on Pharmaceutical Sciences (CRIPS), 2006 Apr;7(2):8-13.(Review Article)<br><br />
<br />
== Poster Presentations ==<br />
1.'''Nair PC''', Malde AK, Mark AE."Validation of fragment hits in X-ray crystal complexes", The East Coast Protein Meeting, Coffs Harbour NSW, Australia, 15-17th July 2011<br />
<br />
2.'''Nair PC''', Malde AK, Mark AE."The structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-methyltransferase (PNMT): A Molecular Dynamics and Free Energy study", Molecular Modelling 2010, Melbourne, Australia, 28Nov-1Dec 2010.<br />
<br />
3.'''Nair PC''', Malde AK, Mark AE.Investigating structural requirements for PNMT inhibition: A molecular dynamics and free energy calculation study", Division of chemistry and structural biology symposium, Institute of Molecular Bioscience, Brisbane, Australia, Nov 18-19 2010.<br />
<br />
4.'''Nair PC''', Malde AK, Mark AE. "Investigation of ligand interaction and binding free Energy of 1,2,3,4 tetrahydroisoquinoline analogues as PNMT inhibitors", 61st Indian Pharmaceutical Congress, 11-13 December 2009.<br />
<br />
5.'''Nair PC''', Sobhia ME. "Identification of Novel CCR2 Scaffolds Through Fingerprint Directed Virtual Screening", Virtual Discovery Europe (Computer Aided Drug Design and Screening) London, England, 24-25 October 2007. (Presented by Dr. M. Elizabeth Sobhia, NIPER )<br />
<br />
6.'''Nair PC''', Sobhia ME. "Synergistic application of target structure based alignment and 3D-QSAR study of protein tyrosine phosphatases 1B (PTP1B) inhibitors", Workshop on Pharmcoinformatics: Tools for Drug Target Identification, NIPER, India, March 14-16, 2007.<br />
<br />
7.'''Nair PC''', Sobhia ME. "Quantitative Structure Toxicity Relationship (QSTR) Studies for Predicting Mutagenicity of Nitro Compounds", International Conference on Chemoinformatics, NCL, Pune, India, Jan 22, 2007.<br />
<br />
8.'''Nair PC''', Sobhia ME. "Design of novel PTP1B inhibitors using 3D-QSAR and concept of hypothetical cavity generation", Workshop on Pharmacoinformatics: QSAR, NIPER, India, March 3-4, 2006.<br />
<br />
== Other Conferences/Scientific visits ==<br />
<br />
Structural Biology Symposium, Institute for Glycomics, Griffith University, Gold Coast, Australia, 2009. <br />
<br />
Molecular Modelling (MM2009), Gold Coast, Queensland, Australia, July 26-29 2009. <br />
<br />
Attended 8th National Center of Competence in Research (NCCR) Practical Course in the area of computational structural biology, Kandersteg, Switzerland, Jan 10-15 2010.<br />
<br />
Visited as a scientific guest in the laboratory of Prof. Wilfred F. van Gunsteren, ETH Zurich, Switzerland, Jan 16-29 2010.<br />
<br />
== Contact Details ==<br />
<br />
Endeavour IPRS Doctoral Fellow <br><br />
Molecular Dynamics Group <br><br />
School of Chemistry and Molecular Biosciences (SCMB) <br><br />
Molecular Biosciences Building (#76) <br><br />
The University of Queensland <br><br />
St. Lucia Campus, Brisbane, QLD 4072 <br><br />
Australia <br><br />
<br />
'''email''' p.nair@uq.edu.au</div>PramodNairhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Pramod_Nair&diff=16050Pramod Nair2012-03-15T06:34:39Z<p>PramodNair: /* Publications */</p>
<hr />
<div>Automated Force Field Topology Builder (ATB) for GROMOS and GROMACS : MD group of Prof. Alan E. Mark<br />
http://compbio.biosci.uq.edu.au/atb/ <br />
<br />
== Research Interests ==<br />
Computer Aided Drug Design (CADD) and Free Energy Calculations<br />
<br />
Alternate Free energy methods to aid high-throughput virtual screening in drug discovery<br />
<br />
Molecular Dynamics simulations of macromolecular and small molecular systems<br />
<br />
== Academic ==<br />
'''B. Pharm.''' Bombay College of Pharmacy, University of Mumbai, India 2001-2005 <br><br />
'''MS (Pharm.)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2005-2007 <br><br />
'''Junior Research Fellow (JRF)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2007-2008 <br><br />
'''PhD Student''' Molecular Dynamics Group, School of Chemistry and Molecular Biosciences (SCMB),University of Queensland, Australia 2009 <br><br />
<br />
== Publications ==<br />
1.'''Nair PC''', Malde AK, Nyssa D, Mark AE. Missing Fragments: Detecting cooperative binding in fragment based drug design. ''ACS Med. Chem. Lett.'' 2012, [http://dx.doi.org/10.1021/ml300015u DOI: 10.1021/ml300015u]<br />
[http://www.rcsb.org/pdb/explore/explore.do?structureId=4DM3 PDBcode 4DM3]<br />
<br />
2. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, '''Nair PC''', Oostenbrink C, Mark AE. An Automated force field Topology Builder (ATB) and repository: version 1.0. ''J Chem Theory Comput.'' 2011, Oct;7(12):4026–4037.[http://dx.doi.org/10.1021/ct200196m DOI: 10.1021/ct200196m]<br />
<br />
3. Riniker S, Christ CD, Hansen N, Mark AE, '''Nair PC''', van Gunsteren WF. Comparison of Enveloping Distribution Sampling and Thermodynamic Integration to Calculate Binding Free Energies of Phenylethanolamine N-Methyltransferase Inhibitors. ''J Chem Phys.'' 2011 Jul;135(2):024105-13. [http://dx.doi.org/10.1063/1.3604534 DOI:10.1063/1.3604534]<br />
<br />
4.'''Nair PC''', Malde AK, Mark AE."Using theory to reconcile experiment: the structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-MethylTransferase (PNMT)". ''J Chem Theory Comput.'' 2011, May;7(5):1458-1468. [http://dx.doi.org/10.1021/ct1007229 DOI: 10.1021/ct1007229]<br />
<br />
5.'''Nair PC'''. "Molecular Field Analysis (MFA) and other QSAR techniques in development of phosphatase inhibitors".<br />
''Anticancer Agents Med Chem.'' 2011 Jan;11(1):151-163. (Invited Review Article) [http://dx.doi.org/10.2174/187152011794941181 DOI: 10.2174/187152011794941181]<br />
<br />
6.'''Nair PC''', Sobhia ME. "Fingerprint directed scaffold hopping for identification of CCR2 antagonists".<br />
''J Chem Inf Model.'' 2008 Sep;48(9):1891-902. [http://dx.doi.org/10.1021/ci800157j DOI: 10.1021/ci800157j]<br />
<br />
7.'''Nair PC''', Srikanth K, Sobhia ME. "QSAR studies on CCR2 antagonists with chiral sensitive hologram descriptors".<br />
''Bioorg Med Chem Lett.'' 2008 Feb;18(4):1323-30. [http://dx.doi.org/10.1016/j.bmcl.2008.01.023 DOI: 10.1016/j.bmcl.2008.01.023]<br />
<br />
8.Srikanth K, '''Nair PC''', Sobhia ME. "Probing the structural and topological requirements for CCR2 antagonism: holographic QSAR for <br> indolopiperidine derivatives".''Bioorg Med Chem Lett.'' 2008 Feb;18(4):1450-6. [http://dx.doi.org/10.1016/j.bmcl.2007.12.072 DOI: 10.1016/j.bmcl.2007.12.072]<br />
<br />
9.'''Nair PC''', Sobhia ME. "Comparative QSTR studies for predicting mutagenicity of nitro compounds".<br />
''J Mol Graph Model.'' 2008 Feb;26(6):916-34. [http://dx.doi.org/10.1016/j.jmgm.2007.06.006 DOI:10.1016/j.jmgm.2007.06.006]<br />
<br />
10.'''Nair PC''', Sobhia ME. "Quantitative structure activity relationship studies on thiourea analogues as influenza virus neuraminidase inhibitors". ''Eur J Med Chem.'' 2008 Feb;43(2):293-9. [http://dx.doi.org/10.1016/j.ejmech.2007.03.020 DOI: 10.1016/j.ejmech.2007.03.020]<br />
<br />
11.'''Nair PC''', Sobhia ME."CoMFA based de novo design of pyridazine analogs as PTP1B inhibitors".<br />
''J Mol Graph Model.'' 2007 Jul;26(1):117-23. [http://dx.doi.org/10.1016/j.jmgm.2006.10.002 DOI: 10.1016/j.jmgm.2006.10.002]<br />
<br />
12.Khurana J, '''Nair P''',Sobhia ME. "Design of Allosteric Ligands Using Computer Aided Drug Design (CADD) Techniques", Current Research & Information on Pharmaceutical Sciences (CRIPS), 2006 Apr;7(2):8-13.(Review Article)<br><br />
<br />
== Poster Presentations ==<br />
1.'''Nair PC''', Malde AK, Mark AE."Validation of fragment hits in X-ray crystal complexes", The East Coast Protein Meeting, Coffs Harbour NSW, Australia, 15-17th July 2011<br />
<br />
2.'''Nair PC''', Malde AK, Mark AE."The structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-methyltransferase (PNMT): A Molecular Dynamics and Free Energy study", Molecular Modelling 2010, Melbourne, Australia, 28Nov-1Dec 2010.<br />
<br />
3.'''Nair PC''', Malde AK, Mark AE.Investigating structural requirements for PNMT inhibition: A molecular dynamics and free energy calculation study", Division of chemistry and structural biology symposium, Institute of Molecular Bioscience, Brisbane, Australia, Nov 18-19 2010.<br />
<br />
4.'''Nair PC''', Malde AK, Mark AE. "Investigation of ligand interaction and binding free Energy of 1,2,3,4 tetrahydroisoquinoline analogues as PNMT inhibitors", 61st Indian Pharmaceutical Congress, 11-13 December 2009.<br />
<br />
5.'''Nair PC''', Sobhia ME. "Identification of Novel CCR2 Scaffolds Through Fingerprint Directed Virtual Screening", Virtual Discovery Europe (Computer Aided Drug Design and Screening) London, England, 24-25 October 2007. (Presented by Dr. M. Elizabeth Sobhia, NIPER )<br />
<br />
6.'''Nair PC''', Sobhia ME. "Synergistic application of target structure based alignment and 3D-QSAR study of protein tyrosine phosphatases 1B (PTP1B) inhibitors", Workshop on Pharmcoinformatics: Tools for Drug Target Identification, NIPER, India, March 14-16, 2007.<br />
<br />
7.'''Nair PC''', Sobhia ME. "Quantitative Structure Toxicity Relationship (QSTR) Studies for Predicting Mutagenicity of Nitro Compounds", International Conference on Chemoinformatics, NCL, Pune, India, Jan 22, 2007.<br />
<br />
8.'''Nair PC''', Sobhia ME. "Design of novel PTP1B inhibitors using 3D-QSAR and concept of hypothetical cavity generation", Workshop on Pharmacoinformatics: QSAR, NIPER, India, March 3-4, 2006.<br />
<br />
== Other Conferences/Scientific visits ==<br />
<br />
Structural Biology Symposium, Institute for Glycomics, Griffith University, Gold Coast, Australia, 2009. <br />
<br />
Molecular Modelling (MM2009), Gold Coast, Queensland, Australia, July 26-29 2009. <br />
<br />
Attended 8th National Center of Competence in Research (NCCR) Practical Course in the area of computational structural biology, Kandersteg, Switzerland, Jan 10-15 2010.<br />
<br />
Visited as a scientific guest in the laboratory of Prof. Wilfred F. van Gunsteren, ETH Zurich, Switzerland, Jan 16-29 2010.<br />
<br />
== Contact Details ==<br />
<br />
Endeavour IPRS Doctoral Fellow <br><br />
Molecular Dynamics Group <br><br />
School of Chemistry and Molecular Biosciences (SCMB) <br><br />
Molecular Biosciences Building (#76) <br><br />
The University of Queensland <br><br />
St. Lucia Campus, Brisbane, QLD 4072 <br><br />
Australia <br><br />
<br />
'''email''' p.nair@uq.edu.au</div>PramodNairhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Pramod_Nair&diff=16049Pramod Nair2012-03-15T06:34:24Z<p>PramodNair: /* Publications */</p>
<hr />
<div>Automated Force Field Topology Builder (ATB) for GROMOS and GROMACS : MD group of Prof. Alan E. Mark<br />
http://compbio.biosci.uq.edu.au/atb/ <br />
<br />
== Research Interests ==<br />
Computer Aided Drug Design (CADD) and Free Energy Calculations<br />
<br />
Alternate Free energy methods to aid high-throughput virtual screening in drug discovery<br />
<br />
Molecular Dynamics simulations of macromolecular and small molecular systems<br />
<br />
== Academic ==<br />
'''B. Pharm.''' Bombay College of Pharmacy, University of Mumbai, India 2001-2005 <br><br />
'''MS (Pharm.)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2005-2007 <br><br />
'''Junior Research Fellow (JRF)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2007-2008 <br><br />
'''PhD Student''' Molecular Dynamics Group, School of Chemistry and Molecular Biosciences (SCMB),University of Queensland, Australia 2009 <br><br />
<br />
== Publications ==<br />
1.'''Nair PC''', Malde AK, Nyssa D, Mark AE. Missing Fragments: Detecting cooperative binding in fragment based drug design. ''ACS Med. Chem. Lett.'' 2012, [http://dx.doi.org/10.1021/ml300015u DOI: 10.1021/ml300015u][http://www.rcsb.org/pdb/explore/explore.do?structureId=4DM3 PDBcode 4DM3]<br />
<br />
2. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, '''Nair PC''', Oostenbrink C, Mark AE. An Automated force field Topology Builder (ATB) and repository: version 1.0. ''J Chem Theory Comput.'' 2011, Oct;7(12):4026–4037.[http://dx.doi.org/10.1021/ct200196m DOI: 10.1021/ct200196m]<br />
<br />
3. Riniker S, Christ CD, Hansen N, Mark AE, '''Nair PC''', van Gunsteren WF. Comparison of Enveloping Distribution Sampling and Thermodynamic Integration to Calculate Binding Free Energies of Phenylethanolamine N-Methyltransferase Inhibitors. ''J Chem Phys.'' 2011 Jul;135(2):024105-13. [http://dx.doi.org/10.1063/1.3604534 DOI:10.1063/1.3604534]<br />
<br />
4.'''Nair PC''', Malde AK, Mark AE."Using theory to reconcile experiment: the structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-MethylTransferase (PNMT)". ''J Chem Theory Comput.'' 2011, May;7(5):1458-1468. [http://dx.doi.org/10.1021/ct1007229 DOI: 10.1021/ct1007229]<br />
<br />
5.'''Nair PC'''. "Molecular Field Analysis (MFA) and other QSAR techniques in development of phosphatase inhibitors".<br />
''Anticancer Agents Med Chem.'' 2011 Jan;11(1):151-163. (Invited Review Article) [http://dx.doi.org/10.2174/187152011794941181 DOI: 10.2174/187152011794941181]<br />
<br />
6.'''Nair PC''', Sobhia ME. "Fingerprint directed scaffold hopping for identification of CCR2 antagonists".<br />
''J Chem Inf Model.'' 2008 Sep;48(9):1891-902. [http://dx.doi.org/10.1021/ci800157j DOI: 10.1021/ci800157j]<br />
<br />
7.'''Nair PC''', Srikanth K, Sobhia ME. "QSAR studies on CCR2 antagonists with chiral sensitive hologram descriptors".<br />
''Bioorg Med Chem Lett.'' 2008 Feb;18(4):1323-30. [http://dx.doi.org/10.1016/j.bmcl.2008.01.023 DOI: 10.1016/j.bmcl.2008.01.023]<br />
<br />
8.Srikanth K, '''Nair PC''', Sobhia ME. "Probing the structural and topological requirements for CCR2 antagonism: holographic QSAR for <br> indolopiperidine derivatives".''Bioorg Med Chem Lett.'' 2008 Feb;18(4):1450-6. [http://dx.doi.org/10.1016/j.bmcl.2007.12.072 DOI: 10.1016/j.bmcl.2007.12.072]<br />
<br />
9.'''Nair PC''', Sobhia ME. "Comparative QSTR studies for predicting mutagenicity of nitro compounds".<br />
''J Mol Graph Model.'' 2008 Feb;26(6):916-34. [http://dx.doi.org/10.1016/j.jmgm.2007.06.006 DOI:10.1016/j.jmgm.2007.06.006]<br />
<br />
10.'''Nair PC''', Sobhia ME. "Quantitative structure activity relationship studies on thiourea analogues as influenza virus neuraminidase inhibitors". ''Eur J Med Chem.'' 2008 Feb;43(2):293-9. [http://dx.doi.org/10.1016/j.ejmech.2007.03.020 DOI: 10.1016/j.ejmech.2007.03.020]<br />
<br />
11.'''Nair PC''', Sobhia ME."CoMFA based de novo design of pyridazine analogs as PTP1B inhibitors".<br />
''J Mol Graph Model.'' 2007 Jul;26(1):117-23. [http://dx.doi.org/10.1016/j.jmgm.2006.10.002 DOI: 10.1016/j.jmgm.2006.10.002]<br />
<br />
12.Khurana J, '''Nair P''',Sobhia ME. "Design of Allosteric Ligands Using Computer Aided Drug Design (CADD) Techniques", Current Research & Information on Pharmaceutical Sciences (CRIPS), 2006 Apr;7(2):8-13.(Review Article)<br><br />
<br />
== Poster Presentations ==<br />
1.'''Nair PC''', Malde AK, Mark AE."Validation of fragment hits in X-ray crystal complexes", The East Coast Protein Meeting, Coffs Harbour NSW, Australia, 15-17th July 2011<br />
<br />
2.'''Nair PC''', Malde AK, Mark AE."The structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-methyltransferase (PNMT): A Molecular Dynamics and Free Energy study", Molecular Modelling 2010, Melbourne, Australia, 28Nov-1Dec 2010.<br />
<br />
3.'''Nair PC''', Malde AK, Mark AE.Investigating structural requirements for PNMT inhibition: A molecular dynamics and free energy calculation study", Division of chemistry and structural biology symposium, Institute of Molecular Bioscience, Brisbane, Australia, Nov 18-19 2010.<br />
<br />
4.'''Nair PC''', Malde AK, Mark AE. "Investigation of ligand interaction and binding free Energy of 1,2,3,4 tetrahydroisoquinoline analogues as PNMT inhibitors", 61st Indian Pharmaceutical Congress, 11-13 December 2009.<br />
<br />
5.'''Nair PC''', Sobhia ME. "Identification of Novel CCR2 Scaffolds Through Fingerprint Directed Virtual Screening", Virtual Discovery Europe (Computer Aided Drug Design and Screening) London, England, 24-25 October 2007. (Presented by Dr. M. Elizabeth Sobhia, NIPER )<br />
<br />
6.'''Nair PC''', Sobhia ME. "Synergistic application of target structure based alignment and 3D-QSAR study of protein tyrosine phosphatases 1B (PTP1B) inhibitors", Workshop on Pharmcoinformatics: Tools for Drug Target Identification, NIPER, India, March 14-16, 2007.<br />
<br />
7.'''Nair PC''', Sobhia ME. "Quantitative Structure Toxicity Relationship (QSTR) Studies for Predicting Mutagenicity of Nitro Compounds", International Conference on Chemoinformatics, NCL, Pune, India, Jan 22, 2007.<br />
<br />
8.'''Nair PC''', Sobhia ME. "Design of novel PTP1B inhibitors using 3D-QSAR and concept of hypothetical cavity generation", Workshop on Pharmacoinformatics: QSAR, NIPER, India, March 3-4, 2006.<br />
<br />
== Other Conferences/Scientific visits ==<br />
<br />
Structural Biology Symposium, Institute for Glycomics, Griffith University, Gold Coast, Australia, 2009. <br />
<br />
Molecular Modelling (MM2009), Gold Coast, Queensland, Australia, July 26-29 2009. <br />
<br />
Attended 8th National Center of Competence in Research (NCCR) Practical Course in the area of computational structural biology, Kandersteg, Switzerland, Jan 10-15 2010.<br />
<br />
Visited as a scientific guest in the laboratory of Prof. Wilfred F. van Gunsteren, ETH Zurich, Switzerland, Jan 16-29 2010.<br />
<br />
== Contact Details ==<br />
<br />
Endeavour IPRS Doctoral Fellow <br><br />
Molecular Dynamics Group <br><br />
School of Chemistry and Molecular Biosciences (SCMB) <br><br />
Molecular Biosciences Building (#76) <br><br />
The University of Queensland <br><br />
St. Lucia Campus, Brisbane, QLD 4072 <br><br />
Australia <br><br />
<br />
'''email''' p.nair@uq.edu.au</div>PramodNairhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Pramod_Nair&diff=16031Pramod Nair2012-02-15T00:09:54Z<p>PramodNair: /* Publications */</p>
<hr />
<div>Automated Force Field Topology Builder (ATB) for GROMOS and GROMACS : MD group of Prof. Alan E. Mark<br />
http://compbio.biosci.uq.edu.au/atb/ <br />
<br />
== Research Interests ==<br />
Computer Aided Drug Design (CADD) and Free Energy Calculations<br />
<br />
Alternate Free energy methods to aid high-throughput virtual screening in drug discovery<br />
<br />
Molecular Dynamics simulations of macromolecular and small molecular systems<br />
<br />
== Academic ==<br />
'''B. Pharm.''' Bombay College of Pharmacy, University of Mumbai, India 2001-2005 <br><br />
'''MS (Pharm.)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2005-2007 <br><br />
'''Junior Research Fellow (JRF)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2007-2008 <br><br />
'''PhD Student''' Molecular Dynamics Group, School of Chemistry and Molecular Biosciences (SCMB),University of Queensland, Australia 2009 <br><br />
<br />
== Publications ==<br />
1.'''Nair PC''', Malde AK, Nyssa D, Mark AE. Missing Fragments: Detecting cooperative binding in fragment based drug design. ''ACS Med. Chem. Lett.'' 2012, [http://dx.doi.org/10.1021/ml300015u DOI: 10.1021/ml300015u]<br />
<br />
2. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, '''Nair PC''', Oostenbrink C, Mark AE. An Automated force field Topology Builder (ATB) and repository: version 1.0. ''J Chem Theory Comput.'' 2011, Oct;7(12):4026–4037.[http://dx.doi.org/10.1021/ct200196m DOI: 10.1021/ct200196m]<br />
<br />
3. Riniker S, Christ CD, Hansen N, Mark AE, '''Nair PC''', van Gunsteren WF. Comparison of Enveloping Distribution Sampling and Thermodynamic Integration to Calculate Binding Free Energies of Phenylethanolamine N-Methyltransferase Inhibitors. ''J Chem Phys.'' 2011 Jul;135(2):024105-13. [http://dx.doi.org/10.1063/1.3604534 DOI:10.1063/1.3604534]<br />
<br />
4.'''Nair PC''', Malde AK, Mark AE."Using theory to reconcile experiment: the structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-MethylTransferase (PNMT)". ''J Chem Theory Comput.'' 2011, May;7(5):1458-1468. [http://dx.doi.org/10.1021/ct1007229 DOI: 10.1021/ct1007229]<br />
<br />
5.'''Nair PC'''. "Molecular Field Analysis (MFA) and other QSAR techniques in development of phosphatase inhibitors".<br />
''Anticancer Agents Med Chem.'' 2011 Jan;11(1):151-163. (Invited Review Article) [http://dx.doi.org/10.2174/187152011794941181 DOI: 10.2174/187152011794941181]<br />
<br />
6.'''Nair PC''', Sobhia ME. "Fingerprint directed scaffold hopping for identification of CCR2 antagonists".<br />
''J Chem Inf Model.'' 2008 Sep;48(9):1891-902. [http://dx.doi.org/10.1021/ci800157j DOI: 10.1021/ci800157j]<br />
<br />
7.'''Nair PC''', Srikanth K, Sobhia ME. "QSAR studies on CCR2 antagonists with chiral sensitive hologram descriptors".<br />
''Bioorg Med Chem Lett.'' 2008 Feb;18(4):1323-30. [http://dx.doi.org/10.1016/j.bmcl.2008.01.023 DOI: 10.1016/j.bmcl.2008.01.023]<br />
<br />
8.Srikanth K, '''Nair PC''', Sobhia ME. "Probing the structural and topological requirements for CCR2 antagonism: holographic QSAR for <br> indolopiperidine derivatives".''Bioorg Med Chem Lett.'' 2008 Feb;18(4):1450-6. [http://dx.doi.org/10.1016/j.bmcl.2007.12.072 DOI: 10.1016/j.bmcl.2007.12.072]<br />
<br />
9.'''Nair PC''', Sobhia ME. "Comparative QSTR studies for predicting mutagenicity of nitro compounds".<br />
''J Mol Graph Model.'' 2008 Feb;26(6):916-34. [http://dx.doi.org/10.1016/j.jmgm.2007.06.006 DOI:10.1016/j.jmgm.2007.06.006]<br />
<br />
10.'''Nair PC''', Sobhia ME. "Quantitative structure activity relationship studies on thiourea analogues as influenza virus neuraminidase inhibitors". ''Eur J Med Chem.'' 2008 Feb;43(2):293-9. [http://dx.doi.org/10.1016/j.ejmech.2007.03.020 DOI: 10.1016/j.ejmech.2007.03.020]<br />
<br />
11.'''Nair PC''', Sobhia ME."CoMFA based de novo design of pyridazine analogs as PTP1B inhibitors".<br />
''J Mol Graph Model.'' 2007 Jul;26(1):117-23. [http://dx.doi.org/10.1016/j.jmgm.2006.10.002 DOI: 10.1016/j.jmgm.2006.10.002]<br />
<br />
12.Khurana J, '''Nair P''',Sobhia ME. "Design of Allosteric Ligands Using Computer Aided Drug Design (CADD) Techniques", Current Research & Information on Pharmaceutical Sciences (CRIPS), 2006 Apr;7(2):8-13.(Review Article)<br><br />
<br />
== Poster Presentations ==<br />
1.'''Nair PC''', Malde AK, Mark AE."Validation of fragment hits in X-ray crystal complexes", The East Coast Protein Meeting, Coffs Harbour NSW, Australia, 15-17th July 2011<br />
<br />
2.'''Nair PC''', Malde AK, Mark AE."The structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-methyltransferase (PNMT): A Molecular Dynamics and Free Energy study", Molecular Modelling 2010, Melbourne, Australia, 28Nov-1Dec 2010.<br />
<br />
3.'''Nair PC''', Malde AK, Mark AE.Investigating structural requirements for PNMT inhibition: A molecular dynamics and free energy calculation study", Division of chemistry and structural biology symposium, Institute of Molecular Bioscience, Brisbane, Australia, Nov 18-19 2010.<br />
<br />
4.'''Nair PC''', Malde AK, Mark AE. "Investigation of ligand interaction and binding free Energy of 1,2,3,4 tetrahydroisoquinoline analogues as PNMT inhibitors", 61st Indian Pharmaceutical Congress, 11-13 December 2009.<br />
<br />
5.'''Nair PC''', Sobhia ME. "Identification of Novel CCR2 Scaffolds Through Fingerprint Directed Virtual Screening", Virtual Discovery Europe (Computer Aided Drug Design and Screening) London, England, 24-25 October 2007. (Presented by Dr. M. Elizabeth Sobhia, NIPER )<br />
<br />
6.'''Nair PC''', Sobhia ME. "Synergistic application of target structure based alignment and 3D-QSAR study of protein tyrosine phosphatases 1B (PTP1B) inhibitors", Workshop on Pharmcoinformatics: Tools for Drug Target Identification, NIPER, India, March 14-16, 2007.<br />
<br />
7.'''Nair PC''', Sobhia ME. "Quantitative Structure Toxicity Relationship (QSTR) Studies for Predicting Mutagenicity of Nitro Compounds", International Conference on Chemoinformatics, NCL, Pune, India, Jan 22, 2007.<br />
<br />
8.'''Nair PC''', Sobhia ME. "Design of novel PTP1B inhibitors using 3D-QSAR and concept of hypothetical cavity generation", Workshop on Pharmacoinformatics: QSAR, NIPER, India, March 3-4, 2006.<br />
<br />
== Other Conferences/Scientific visits ==<br />
<br />
Structural Biology Symposium, Institute for Glycomics, Griffith University, Gold Coast, Australia, 2009. <br />
<br />
Molecular Modelling (MM2009), Gold Coast, Queensland, Australia, July 26-29 2009. <br />
<br />
Attended 8th National Center of Competence in Research (NCCR) Practical Course in the area of computational structural biology, Kandersteg, Switzerland, Jan 10-15 2010.<br />
<br />
Visited as a scientific guest in the laboratory of Prof. Wilfred F. van Gunsteren, ETH Zurich, Switzerland, Jan 16-29 2010.<br />
<br />
== Contact Details ==<br />
<br />
Endeavour IPRS Doctoral Fellow <br><br />
Molecular Dynamics Group <br><br />
School of Chemistry and Molecular Biosciences (SCMB) <br><br />
Molecular Biosciences Building (#76) <br><br />
The University of Queensland <br><br />
St. Lucia Campus, Brisbane, QLD 4072 <br><br />
Australia <br><br />
<br />
'''email''' p.nair@uq.edu.au</div>PramodNairhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Pramod_Nair&diff=16030Pramod Nair2012-02-15T00:09:11Z<p>PramodNair: /* Publications */</p>
<hr />
<div>Automated Force Field Topology Builder (ATB) for GROMOS and GROMACS : MD group of Prof. Alan E. Mark<br />
http://compbio.biosci.uq.edu.au/atb/ <br />
<br />
== Research Interests ==<br />
Computer Aided Drug Design (CADD) and Free Energy Calculations<br />
<br />
Alternate Free energy methods to aid high-throughput virtual screening in drug discovery<br />
<br />
Molecular Dynamics simulations of macromolecular and small molecular systems<br />
<br />
== Academic ==<br />
'''B. Pharm.''' Bombay College of Pharmacy, University of Mumbai, India 2001-2005 <br><br />
'''MS (Pharm.)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2005-2007 <br><br />
'''Junior Research Fellow (JRF)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2007-2008 <br><br />
'''PhD Student''' Molecular Dynamics Group, School of Chemistry and Molecular Biosciences (SCMB),University of Queensland, Australia 2009 <br><br />
<br />
== Publications ==<br />
1.'''Nair PC''', Malde AK, Nyssa D, Mark AE.Missing Fragments: Detecting cooperative binding in fragment based drug design. ''ACS Med. Chem. Lett.'' 2012, [http://dx.doi.org/10.1021/ml300015u DOI: 10.1021/ml300015u]<br />
<br />
2. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, '''Nair PC''', Oostenbrink C, Mark AE. An Automated force field Topology Builder (ATB) and repository: version 1.0. ''J Chem Theory Comput.'' 2011, Oct;7(12):4026–4037.[http://dx.doi.org/10.1021/ct200196m DOI: 10.1021/ct200196m]<br />
<br />
3. Riniker S, Christ CD, Hansen N, Mark AE, '''Nair PC''', van Gunsteren WF. Comparison of Enveloping Distribution Sampling and Thermodynamic Integration to Calculate Binding Free Energies of Phenylethanolamine N-Methyltransferase Inhibitors. ''J Chem Phys.'' 2011 Jul;135(2):024105-13. [http://dx.doi.org/10.1063/1.3604534 DOI:10.1063/1.3604534]<br />
<br />
4.'''Nair PC''', Malde AK, Mark AE."Using theory to reconcile experiment: the structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-MethylTransferase (PNMT)". ''J Chem Theory Comput.'' 2011, May;7(5):1458-1468. [http://dx.doi.org/10.1021/ct1007229 DOI: 10.1021/ct1007229]<br />
<br />
5.'''Nair PC'''. "Molecular Field Analysis (MFA) and other QSAR techniques in development of phosphatase inhibitors".<br />
''Anticancer Agents Med Chem.'' 2011 Jan;11(1):151-163. (Invited Review Article) [http://dx.doi.org/10.2174/187152011794941181 DOI: 10.2174/187152011794941181]<br />
<br />
6.'''Nair PC''', Sobhia ME. "Fingerprint directed scaffold hopping for identification of CCR2 antagonists".<br />
''J Chem Inf Model.'' 2008 Sep;48(9):1891-902. [http://dx.doi.org/10.1021/ci800157j DOI: 10.1021/ci800157j]<br />
<br />
7.'''Nair PC''', Srikanth K, Sobhia ME. "QSAR studies on CCR2 antagonists with chiral sensitive hologram descriptors".<br />
''Bioorg Med Chem Lett.'' 2008 Feb;18(4):1323-30. [http://dx.doi.org/10.1016/j.bmcl.2008.01.023 DOI: 10.1016/j.bmcl.2008.01.023]<br />
<br />
8.Srikanth K, '''Nair PC''', Sobhia ME. "Probing the structural and topological requirements for CCR2 antagonism: holographic QSAR for <br> indolopiperidine derivatives".''Bioorg Med Chem Lett.'' 2008 Feb;18(4):1450-6. [http://dx.doi.org/10.1016/j.bmcl.2007.12.072 DOI: 10.1016/j.bmcl.2007.12.072]<br />
<br />
9.'''Nair PC''', Sobhia ME. "Comparative QSTR studies for predicting mutagenicity of nitro compounds".<br />
''J Mol Graph Model.'' 2008 Feb;26(6):916-34. [http://dx.doi.org/10.1016/j.jmgm.2007.06.006 DOI:10.1016/j.jmgm.2007.06.006]<br />
<br />
10.'''Nair PC''', Sobhia ME. "Quantitative structure activity relationship studies on thiourea analogues as influenza virus neuraminidase inhibitors". ''Eur J Med Chem.'' 2008 Feb;43(2):293-9. [http://dx.doi.org/10.1016/j.ejmech.2007.03.020 DOI: 10.1016/j.ejmech.2007.03.020]<br />
<br />
11.'''Nair PC''', Sobhia ME."CoMFA based de novo design of pyridazine analogs as PTP1B inhibitors".<br />
''J Mol Graph Model.'' 2007 Jul;26(1):117-23. [http://dx.doi.org/10.1016/j.jmgm.2006.10.002 DOI: 10.1016/j.jmgm.2006.10.002]<br />
<br />
12.Khurana J, '''Nair P''',Sobhia ME. "Design of Allosteric Ligands Using Computer Aided Drug Design (CADD) Techniques", Current Research & Information on Pharmaceutical Sciences (CRIPS), 2006 Apr;7(2):8-13.(Review Article)<br><br />
<br />
== Poster Presentations ==<br />
1.'''Nair PC''', Malde AK, Mark AE."Validation of fragment hits in X-ray crystal complexes", The East Coast Protein Meeting, Coffs Harbour NSW, Australia, 15-17th July 2011<br />
<br />
2.'''Nair PC''', Malde AK, Mark AE."The structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-methyltransferase (PNMT): A Molecular Dynamics and Free Energy study", Molecular Modelling 2010, Melbourne, Australia, 28Nov-1Dec 2010.<br />
<br />
3.'''Nair PC''', Malde AK, Mark AE.Investigating structural requirements for PNMT inhibition: A molecular dynamics and free energy calculation study", Division of chemistry and structural biology symposium, Institute of Molecular Bioscience, Brisbane, Australia, Nov 18-19 2010.<br />
<br />
4.'''Nair PC''', Malde AK, Mark AE. "Investigation of ligand interaction and binding free Energy of 1,2,3,4 tetrahydroisoquinoline analogues as PNMT inhibitors", 61st Indian Pharmaceutical Congress, 11-13 December 2009.<br />
<br />
5.'''Nair PC''', Sobhia ME. "Identification of Novel CCR2 Scaffolds Through Fingerprint Directed Virtual Screening", Virtual Discovery Europe (Computer Aided Drug Design and Screening) London, England, 24-25 October 2007. (Presented by Dr. M. Elizabeth Sobhia, NIPER )<br />
<br />
6.'''Nair PC''', Sobhia ME. "Synergistic application of target structure based alignment and 3D-QSAR study of protein tyrosine phosphatases 1B (PTP1B) inhibitors", Workshop on Pharmcoinformatics: Tools for Drug Target Identification, NIPER, India, March 14-16, 2007.<br />
<br />
7.'''Nair PC''', Sobhia ME. "Quantitative Structure Toxicity Relationship (QSTR) Studies for Predicting Mutagenicity of Nitro Compounds", International Conference on Chemoinformatics, NCL, Pune, India, Jan 22, 2007.<br />
<br />
8.'''Nair PC''', Sobhia ME. "Design of novel PTP1B inhibitors using 3D-QSAR and concept of hypothetical cavity generation", Workshop on Pharmacoinformatics: QSAR, NIPER, India, March 3-4, 2006.<br />
<br />
== Other Conferences/Scientific visits ==<br />
<br />
Structural Biology Symposium, Institute for Glycomics, Griffith University, Gold Coast, Australia, 2009. <br />
<br />
Molecular Modelling (MM2009), Gold Coast, Queensland, Australia, July 26-29 2009. <br />
<br />
Attended 8th National Center of Competence in Research (NCCR) Practical Course in the area of computational structural biology, Kandersteg, Switzerland, Jan 10-15 2010.<br />
<br />
Visited as a scientific guest in the laboratory of Prof. Wilfred F. van Gunsteren, ETH Zurich, Switzerland, Jan 16-29 2010.<br />
<br />
== Contact Details ==<br />
<br />
Endeavour IPRS Doctoral Fellow <br><br />
Molecular Dynamics Group <br><br />
School of Chemistry and Molecular Biosciences (SCMB) <br><br />
Molecular Biosciences Building (#76) <br><br />
The University of Queensland <br><br />
St. Lucia Campus, Brisbane, QLD 4072 <br><br />
Australia <br><br />
<br />
'''email''' p.nair@uq.edu.au</div>PramodNairhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Pramod_Nair&diff=16026Pramod Nair2012-01-31T15:17:12Z<p>PramodNair: /* Publications */</p>
<hr />
<div>Automated Force Field Topology Builder (ATB) for GROMOS and GROMACS : MD group of Prof. Alan E. Mark<br />
http://compbio.biosci.uq.edu.au/atb/ <br />
<br />
== Research Interests ==<br />
Computer Aided Drug Design (CADD) and Free Energy Calculations<br />
<br />
Alternate Free energy methods to aid high-throughput virtual screening in drug discovery<br />
<br />
Molecular Dynamics simulations of macromolecular and small molecular systems<br />
<br />
== Academic ==<br />
'''B. Pharm.''' Bombay College of Pharmacy, University of Mumbai, India 2001-2005 <br><br />
'''MS (Pharm.)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2005-2007 <br><br />
'''Junior Research Fellow (JRF)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2007-2008 <br><br />
'''PhD Student''' Molecular Dynamics Group, School of Chemistry and Molecular Biosciences (SCMB),University of Queensland, Australia 2009 <br><br />
<br />
== Publications ==<br />
1. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, '''Nair PC''', Oostenbrink C, Mark AE. An Automated force field Topology Builder (ATB) and repository: version 1.0. ''J Chem Theory Comput.'' 2011, Oct;7(12):4026–4037.[http://dx.doi.org/10.1021/ct200196m DOI: 10.1021/ct200196m]<br />
<br />
2. Riniker S, Christ CD, Hansen N, Mark AE, '''Nair PC''', van Gunsteren WF. Comparison of Enveloping Distribution Sampling and Thermodynamic Integration to Calculate Binding Free Energies of Phenylethanolamine N-Methyltransferase Inhibitors. ''J Chem Phys.'' 2011 Jul;135(2):024105-13. [http://dx.doi.org/10.1063/1.3604534 DOI:10.1063/1.3604534]<br />
<br />
3.'''Nair PC''', Malde AK, Mark AE."Using theory to reconcile experiment: the structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-MethylTransferase (PNMT)". ''J Chem Theory Comput.'' 2011, May;7(5):1458-1468. [http://dx.doi.org/10.1021/ct1007229 DOI: 10.1021/ct1007229]<br />
<br />
4.'''Nair PC'''. "Molecular Field Analysis (MFA) and other QSAR techniques in development of phosphatase inhibitors".<br />
''Anticancer Agents Med Chem.'' 2011 Jan;11(1):151-163. (Invited Review Article) [http://dx.doi.org/10.2174/187152011794941181 DOI: 10.2174/187152011794941181]<br />
<br />
5.'''Nair PC''', Sobhia ME. "Fingerprint directed scaffold hopping for identification of CCR2 antagonists".<br />
''J Chem Inf Model.'' 2008 Sep;48(9):1891-902. [http://dx.doi.org/10.1021/ci800157j DOI: 10.1021/ci800157j]<br />
<br />
6.'''Nair PC''', Srikanth K, Sobhia ME. "QSAR studies on CCR2 antagonists with chiral sensitive hologram descriptors".<br />
''Bioorg Med Chem Lett.'' 2008 Feb;18(4):1323-30. [http://dx.doi.org/10.1016/j.bmcl.2008.01.023 DOI: 10.1016/j.bmcl.2008.01.023]<br />
<br />
7.Srikanth K, '''Nair PC''', Sobhia ME. "Probing the structural and topological requirements for CCR2 antagonism: holographic QSAR for <br> indolopiperidine derivatives".''Bioorg Med Chem Lett.'' 2008 Feb;18(4):1450-6. [http://dx.doi.org/10.1016/j.bmcl.2007.12.072 DOI: 10.1016/j.bmcl.2007.12.072]<br />
<br />
8.'''Nair PC''', Sobhia ME. "Comparative QSTR studies for predicting mutagenicity of nitro compounds".<br />
''J Mol Graph Model.'' 2008 Feb;26(6):916-34. [http://dx.doi.org/10.1016/j.jmgm.2007.06.006 DOI:10.1016/j.jmgm.2007.06.006]<br />
<br />
9.'''Nair PC''', Sobhia ME. "Quantitative structure activity relationship studies on thiourea analogues as influenza virus neuraminidase inhibitors". ''Eur J Med Chem.'' 2008 Feb;43(2):293-9. [http://dx.doi.org/10.1016/j.ejmech.2007.03.020 DOI: 10.1016/j.ejmech.2007.03.020]<br />
<br />
10.'''Nair PC''', Sobhia ME."CoMFA based de novo design of pyridazine analogs as PTP1B inhibitors".<br />
''J Mol Graph Model.'' 2007 Jul;26(1):117-23. [http://dx.doi.org/10.1016/j.jmgm.2006.10.002 DOI: 10.1016/j.jmgm.2006.10.002]<br />
<br />
11.Khurana J, '''Nair P''',Sobhia ME. "Design of Allosteric Ligands Using Computer Aided Drug Design (CADD) Techniques", Current Research & Information on Pharmaceutical Sciences (CRIPS), 2006 Apr;7(2):8-13.(Review Article)<br><br />
<br />
== Poster Presentations ==<br />
1.'''Nair PC''', Malde AK, Mark AE."Validation of fragment hits in X-ray crystal complexes", The East Coast Protein Meeting, Coffs Harbour NSW, Australia, 15-17th July 2011<br />
<br />
2.'''Nair PC''', Malde AK, Mark AE."The structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-methyltransferase (PNMT): A Molecular Dynamics and Free Energy study", Molecular Modelling 2010, Melbourne, Australia, 28Nov-1Dec 2010.<br />
<br />
3.'''Nair PC''', Malde AK, Mark AE.Investigating structural requirements for PNMT inhibition: A molecular dynamics and free energy calculation study", Division of chemistry and structural biology symposium, Institute of Molecular Bioscience, Brisbane, Australia, Nov 18-19 2010.<br />
<br />
4.'''Nair PC''', Malde AK, Mark AE. "Investigation of ligand interaction and binding free Energy of 1,2,3,4 tetrahydroisoquinoline analogues as PNMT inhibitors", 61st Indian Pharmaceutical Congress, 11-13 December 2009.<br />
<br />
5.'''Nair PC''', Sobhia ME. "Identification of Novel CCR2 Scaffolds Through Fingerprint Directed Virtual Screening", Virtual Discovery Europe (Computer Aided Drug Design and Screening) London, England, 24-25 October 2007. (Presented by Dr. M. Elizabeth Sobhia, NIPER )<br />
<br />
6.'''Nair PC''', Sobhia ME. "Synergistic application of target structure based alignment and 3D-QSAR study of protein tyrosine phosphatases 1B (PTP1B) inhibitors", Workshop on Pharmcoinformatics: Tools for Drug Target Identification, NIPER, India, March 14-16, 2007.<br />
<br />
7.'''Nair PC''', Sobhia ME. "Quantitative Structure Toxicity Relationship (QSTR) Studies for Predicting Mutagenicity of Nitro Compounds", International Conference on Chemoinformatics, NCL, Pune, India, Jan 22, 2007.<br />
<br />
8.'''Nair PC''', Sobhia ME. "Design of novel PTP1B inhibitors using 3D-QSAR and concept of hypothetical cavity generation", Workshop on Pharmacoinformatics: QSAR, NIPER, India, March 3-4, 2006.<br />
<br />
== Other Conferences/Scientific visits ==<br />
<br />
Structural Biology Symposium, Institute for Glycomics, Griffith University, Gold Coast, Australia, 2009. <br />
<br />
Molecular Modelling (MM2009), Gold Coast, Queensland, Australia, July 26-29 2009. <br />
<br />
Attended 8th National Center of Competence in Research (NCCR) Practical Course in the area of computational structural biology, Kandersteg, Switzerland, Jan 10-15 2010.<br />
<br />
Visited as a scientific guest in the laboratory of Prof. Wilfred F. van Gunsteren, ETH Zurich, Switzerland, Jan 16-29 2010.<br />
<br />
== Contact Details ==<br />
<br />
Endeavour IPRS Doctoral Fellow <br><br />
Molecular Dynamics Group <br><br />
School of Chemistry and Molecular Biosciences (SCMB) <br><br />
Molecular Biosciences Building (#76) <br><br />
The University of Queensland <br><br />
St. Lucia Campus, Brisbane, QLD 4072 <br><br />
Australia <br><br />
<br />
'''email''' p.nair@uq.edu.au</div>PramodNairhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Pramod_Nair&diff=16025Pramod Nair2012-01-31T15:16:48Z<p>PramodNair: /* Publications */</p>
<hr />
<div>Automated Force Field Topology Builder (ATB) for GROMOS and GROMACS : MD group of Prof. Alan E. Mark<br />
http://compbio.biosci.uq.edu.au/atb/ <br />
<br />
== Research Interests ==<br />
Computer Aided Drug Design (CADD) and Free Energy Calculations<br />
<br />
Alternate Free energy methods to aid high-throughput virtual screening in drug discovery<br />
<br />
Molecular Dynamics simulations of macromolecular and small molecular systems<br />
<br />
== Academic ==<br />
'''B. Pharm.''' Bombay College of Pharmacy, University of Mumbai, India 2001-2005 <br><br />
'''MS (Pharm.)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2005-2007 <br><br />
'''Junior Research Fellow (JRF)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2007-2008 <br><br />
'''PhD Student''' Molecular Dynamics Group, School of Chemistry and Molecular Biosciences (SCMB),University of Queensland, Australia 2009 <br><br />
<br />
== Publications ==<br />
1. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, '''Nair PC''', Oostenbrink C, Mark AE. An Automated force field Topology Builder (ATB) and repository: version 1.0. ''J Chem Theory Comput.'' 2011, Oct;7(12)4026–4037:.[http://dx.doi.org/10.1021/ct200196m DOI: 10.1021/ct200196m]<br />
<br />
2. Riniker S, Christ CD, Hansen N, Mark AE, '''Nair PC''', van Gunsteren WF. Comparison of Enveloping Distribution Sampling and Thermodynamic Integration to Calculate Binding Free Energies of Phenylethanolamine N-Methyltransferase Inhibitors. ''J Chem Phys.'' 2011 Jul;135(2):024105-13. [http://dx.doi.org/10.1063/1.3604534 DOI:10.1063/1.3604534]<br />
<br />
3.'''Nair PC''', Malde AK, Mark AE."Using theory to reconcile experiment: the structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-MethylTransferase (PNMT)". ''J Chem Theory Comput.'' 2011, May;7(5):1458-1468. [http://dx.doi.org/10.1021/ct1007229 DOI: 10.1021/ct1007229]<br />
<br />
4.'''Nair PC'''. "Molecular Field Analysis (MFA) and other QSAR techniques in development of phosphatase inhibitors".<br />
''Anticancer Agents Med Chem.'' 2011 Jan;11(1):151-163. (Invited Review Article) [http://dx.doi.org/10.2174/187152011794941181 DOI: 10.2174/187152011794941181]<br />
<br />
5.'''Nair PC''', Sobhia ME. "Fingerprint directed scaffold hopping for identification of CCR2 antagonists".<br />
''J Chem Inf Model.'' 2008 Sep;48(9):1891-902. [http://dx.doi.org/10.1021/ci800157j DOI: 10.1021/ci800157j]<br />
<br />
6.'''Nair PC''', Srikanth K, Sobhia ME. "QSAR studies on CCR2 antagonists with chiral sensitive hologram descriptors".<br />
''Bioorg Med Chem Lett.'' 2008 Feb;18(4):1323-30. [http://dx.doi.org/10.1016/j.bmcl.2008.01.023 DOI: 10.1016/j.bmcl.2008.01.023]<br />
<br />
7.Srikanth K, '''Nair PC''', Sobhia ME. "Probing the structural and topological requirements for CCR2 antagonism: holographic QSAR for <br> indolopiperidine derivatives".''Bioorg Med Chem Lett.'' 2008 Feb;18(4):1450-6. [http://dx.doi.org/10.1016/j.bmcl.2007.12.072 DOI: 10.1016/j.bmcl.2007.12.072]<br />
<br />
8.'''Nair PC''', Sobhia ME. "Comparative QSTR studies for predicting mutagenicity of nitro compounds".<br />
''J Mol Graph Model.'' 2008 Feb;26(6):916-34. [http://dx.doi.org/10.1016/j.jmgm.2007.06.006 DOI:10.1016/j.jmgm.2007.06.006]<br />
<br />
9.'''Nair PC''', Sobhia ME. "Quantitative structure activity relationship studies on thiourea analogues as influenza virus neuraminidase inhibitors". ''Eur J Med Chem.'' 2008 Feb;43(2):293-9. [http://dx.doi.org/10.1016/j.ejmech.2007.03.020 DOI: 10.1016/j.ejmech.2007.03.020]<br />
<br />
10.'''Nair PC''', Sobhia ME."CoMFA based de novo design of pyridazine analogs as PTP1B inhibitors".<br />
''J Mol Graph Model.'' 2007 Jul;26(1):117-23. [http://dx.doi.org/10.1016/j.jmgm.2006.10.002 DOI: 10.1016/j.jmgm.2006.10.002]<br />
<br />
11.Khurana J, '''Nair P''',Sobhia ME. "Design of Allosteric Ligands Using Computer Aided Drug Design (CADD) Techniques", Current Research & Information on Pharmaceutical Sciences (CRIPS), 2006 Apr;7(2):8-13.(Review Article)<br><br />
<br />
== Poster Presentations ==<br />
1.'''Nair PC''', Malde AK, Mark AE."Validation of fragment hits in X-ray crystal complexes", The East Coast Protein Meeting, Coffs Harbour NSW, Australia, 15-17th July 2011<br />
<br />
2.'''Nair PC''', Malde AK, Mark AE."The structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-methyltransferase (PNMT): A Molecular Dynamics and Free Energy study", Molecular Modelling 2010, Melbourne, Australia, 28Nov-1Dec 2010.<br />
<br />
3.'''Nair PC''', Malde AK, Mark AE.Investigating structural requirements for PNMT inhibition: A molecular dynamics and free energy calculation study", Division of chemistry and structural biology symposium, Institute of Molecular Bioscience, Brisbane, Australia, Nov 18-19 2010.<br />
<br />
4.'''Nair PC''', Malde AK, Mark AE. "Investigation of ligand interaction and binding free Energy of 1,2,3,4 tetrahydroisoquinoline analogues as PNMT inhibitors", 61st Indian Pharmaceutical Congress, 11-13 December 2009.<br />
<br />
5.'''Nair PC''', Sobhia ME. "Identification of Novel CCR2 Scaffolds Through Fingerprint Directed Virtual Screening", Virtual Discovery Europe (Computer Aided Drug Design and Screening) London, England, 24-25 October 2007. (Presented by Dr. M. Elizabeth Sobhia, NIPER )<br />
<br />
6.'''Nair PC''', Sobhia ME. "Synergistic application of target structure based alignment and 3D-QSAR study of protein tyrosine phosphatases 1B (PTP1B) inhibitors", Workshop on Pharmcoinformatics: Tools for Drug Target Identification, NIPER, India, March 14-16, 2007.<br />
<br />
7.'''Nair PC''', Sobhia ME. "Quantitative Structure Toxicity Relationship (QSTR) Studies for Predicting Mutagenicity of Nitro Compounds", International Conference on Chemoinformatics, NCL, Pune, India, Jan 22, 2007.<br />
<br />
8.'''Nair PC''', Sobhia ME. "Design of novel PTP1B inhibitors using 3D-QSAR and concept of hypothetical cavity generation", Workshop on Pharmacoinformatics: QSAR, NIPER, India, March 3-4, 2006.<br />
<br />
== Other Conferences/Scientific visits ==<br />
<br />
Structural Biology Symposium, Institute for Glycomics, Griffith University, Gold Coast, Australia, 2009. <br />
<br />
Molecular Modelling (MM2009), Gold Coast, Queensland, Australia, July 26-29 2009. <br />
<br />
Attended 8th National Center of Competence in Research (NCCR) Practical Course in the area of computational structural biology, Kandersteg, Switzerland, Jan 10-15 2010.<br />
<br />
Visited as a scientific guest in the laboratory of Prof. Wilfred F. van Gunsteren, ETH Zurich, Switzerland, Jan 16-29 2010.<br />
<br />
== Contact Details ==<br />
<br />
Endeavour IPRS Doctoral Fellow <br><br />
Molecular Dynamics Group <br><br />
School of Chemistry and Molecular Biosciences (SCMB) <br><br />
Molecular Biosciences Building (#76) <br><br />
The University of Queensland <br><br />
St. Lucia Campus, Brisbane, QLD 4072 <br><br />
Australia <br><br />
<br />
'''email''' p.nair@uq.edu.au</div>PramodNairhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Meeting_schedule&diff=16001Meeting schedule2011-11-16T10:24:47Z<p>PramodNair: /* MD Group Meetings */</p>
<hr />
<div>== MD Group Meetings ==<br />
<br />
This is the current MD Group/BmM Group meeting schedule. This is the '''most up-to-date version'''.<br />
*Please '''do not edit this''' without informing David<br />
*Please '''add you talks''' for archive and reference reasons. This can be achieved by uploading the file (left hand toolbox) and linking to it.<br />
** If you get complaints about file size being to large - simply click upload anyway.<br />
<br />
<br />
''If you would like someone from another lab to give a seminar, you are welcome to suggest a (some) name(s). In this case, it would be a longer seminar (40-45 min + questions).''<br />
<br />
<br />
* The meetings are held on Thursdays, ''every week at <u>10:30 am</u>''.<br />
* The speakers are invited to present a '''research and/or a literature seminar or a conference report for example'''. This is left to their discretion (it's really up to you). ''Talks are 20 min long each (+ questions).''<br>For the days when there is a '''journal club or a theoretical seminar''', one speaker is scheduled. ''For journal clubs and theoretical seminars, the talk should last about 30&ndash;40 min (+ questions).'' <u>Theoretical seminars and journal clubs may need a significant amount of work to be prepared so it is better for the speakers to choose their topic/journal articles well in advance (a few weeks before).</u> Also, the speakers should communicate the article they recommend to read 1 week before the seminar.<br />
* For the Journal Club and the Theoretical Seminars, suggestions of articles can be made on the dedicated wiki pages:<br />
** [[Theoretical Seminars]]<br />
** [[Journal Club]]<br />
* The joint meeting with Bostjan Kobe's, Justin Hill's, Luke Guddat's, Mikael Bod&eacute;n's and Horst Schirra's groups are every last Wednesday of the month in the seminar room of the AIBN from 9 am to 11 am. There are 2 speakers per meeting. Talks should be 15-20 minutes long (+ discussion).<br />
<br />
<br />
{| border="0" cellpadding="5" cellspacing="2"<br />
|- style="background:#c9c9c9"<br />
| style="width:100px"|Date<br />
| style="width:250px"|Speakers<br />
|- <br />
| 31.03.11 || Megan<br />
|- style="background:#c2fbd1"<br />
| 07.04.11 || ''Journal Club''<br />
|-<br />
| 14.04.11 || Patricio<br />
|-<br />
| 21.04.11 || ''Cancelled''<br />
|-<br />
| 28.04.11 || ''Cancelled''<br />
|-<br />
| 05.05.11 || Lara<br />
|- style="background:#c2fbd1"<br />
| 12.05.11 || ''Journal Club''<br />
|-<br />
| 19.05.11 || Seth<br />
|- style="background:#fbc3c3"<br />
| 25.05.11 || David ''(Joint group meeting)''<br />
|-<br />
| 26.05.11 || Pramod<br />
|- style="background:#c2fbd1"<br />
| 02.06.11 || ''Journal Club''<br />
|-<br />
| 09.06.11 || Guang<br />
|- style="background:#cee7fb"<br />
| 16.06.11 || Alpesh ''(Theoretical Seminar)''<br />
|-<br />
| 23.06.11 || ''Cancelled''<br />
|-<br />
| 30.06.11 || Megan<br />
|- style="background:#c2fbd1"<br />
| 07.07.11 || ''Journal Club''<br />
|-<br />
| <font color=#0000ff>1</font><font color=#ff0000>4</font>.<font color=#0000ff>0</font><font color=#ff0000>7</font>.<font color=#0000ff>1</font><font color=#ff0000>1</font> || David (''<font color=#0000ff>Bastille</font> <font color=#ff0000>Day</font>'')<br />
|-<br />
| 21.07.11 || Lachlan<br />
|- style="background:#e4b1fc"<br />
| 27.07.11 || Megan ''(Structural Biology Forum)''<br />
|- style="background:#cee7fb"<br />
| 28.07.11 || Lara ''(Theoretical Seminar)''<br />
|-<br />
| 04.08.11 || Guest speaker: Stephen Fairweather<br />
|- style="background:#c2fbd1"<br />
| 11.08.11 || ''Journal Club''<br />
|-<br />
| 18.08.11 || Pramod<br />
|-<br />
| 25.08.11 || Guang<br />
|- style="background:#c2fbd1"<br />
| 01.09.11 || ''Journal Club''<br />
|-<br />
| 08.09.11 || Lachlan<br />
|- style="background:#e4b1fc"<br />
| 15.09.11 || David ''(COMBIO seminar)''<br />
|-<br />
| 15.09.11 || Lara<br />
|-<br />
| 22.09.11 || ''Cancelled (Group outing)''<br />
|- style="background:#fbc3c3"<br />
| 28.09.10 || Pramod ''(Joint group meeting)''<br />
|-<br />
| 29.09.11 || ''Cancelled''<br />
|-<br />
| 06.10.11 || Guest speaker: Quentin Kaas<br />
|-<br />
| 13.10.11 || Alpesh<br />
|- style="background:#c2fbd1"<br />
| 20.10.11 || ''Journal Club''<br />
|-<br />
| 27.10.11 || David<br />
|-<br />
| 03.11.11 || Guest speaker: Andrew Brooks<br />
|- style="background:#f0e68c"<br />
| 10.11.11 || ''IMB Division of Chemistry and Structural Biology Symposium (all day)''<br />
|- style="background:#e4b1fc"<br />
| 16.11.11 || David ''(Structural Biology Forum)''<br />
|-<br />
| 17.11.11 || Megan<br />
|-<br />
| 24.11.11 || Lachlan [Pramod (School Symposium)]<br />
|-<br />
| 01.12.11 || Guang<br />
|- style="background:#c2fbd1"<br />
| 08.12.11 || ''Journal Club''<br />
|- style="background:#ffff00"<br />
| colspan="2" style="color:#ff0000" align="center"| '''''Summer/Christmas Break'''''<br>''(back in February 2012)''<br />
|}<br />
<br />
== Other important dates ==<br />
<br />
== Items to Discuss at the Next Meeting ==</div>PramodNairhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Pramod_Nair&diff=16000Pramod Nair2011-11-16T00:35:08Z<p>PramodNair: /* Publications */</p>
<hr />
<div>Automated Force Field Topology Builder (ATB) for GROMOS and GROMACS : MD group of Prof. Alan E. Mark<br />
http://compbio.biosci.uq.edu.au/atb/ <br />
<br />
== Research Interests ==<br />
Computer Aided Drug Design (CADD) and Free Energy Calculations<br />
<br />
Alternate Free energy methods to aid high-throughput virtual screening in drug discovery<br />
<br />
Molecular Dynamics simulations of macromolecular and small molecular systems<br />
<br />
== Academic ==<br />
'''B. Pharm.''' Bombay College of Pharmacy, University of Mumbai, India 2001-2005 <br><br />
'''MS (Pharm.)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2005-2007 <br><br />
'''Junior Research Fellow (JRF)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2007-2008 <br><br />
'''PhD Student''' Molecular Dynamics Group, School of Chemistry and Molecular Biosciences (SCMB),University of Queensland, Australia 2009 <br><br />
<br />
== Publications ==<br />
1. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, '''Nair PC''', Oostenbrink C, Mark AE. An Automated force field Topology Builder (ATB) and repository: version 1.0. ''J Chem Theory Comput.'' 2011, In press.[http://dx.doi.org/10.1021/ct200196m DOI: 10.1021/ct200196m]<br />
<br />
2. Riniker S, Christ CD, Hansen N, Mark AE, '''Nair PC''', van Gunsteren WF. Comparison of Enveloping Distribution Sampling and Thermodynamic Integration to Calculate Binding Free Energies of Phenylethanolamine N-Methyltransferase Inhibitors. ''J Chem Phys.'' 2011 Jul;135(2):024105-13. [http://dx.doi.org/10.1063/1.3604534 DOI:10.1063/1.3604534]<br />
<br />
3.'''Nair PC''', Malde AK, Mark AE."Using theory to reconcile experiment: the structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-MethylTransferase (PNMT)". ''J Chem Theory Comput.'' 2011, May;7(5):1458-1468. [http://dx.doi.org/10.1021/ct1007229 DOI: 10.1021/ct1007229]<br />
<br />
4.'''Nair PC'''. "Molecular Field Analysis (MFA) and other QSAR techniques in development of phosphatase inhibitors".<br />
''Anticancer Agents Med Chem.'' 2011 Jan;11(1):151-163. (Invited Review Article) [http://dx.doi.org/10.2174/187152011794941181 DOI: 10.2174/187152011794941181]<br />
<br />
5.'''Nair PC''', Sobhia ME. "Fingerprint directed scaffold hopping for identification of CCR2 antagonists".<br />
''J Chem Inf Model.'' 2008 Sep;48(9):1891-902. [http://dx.doi.org/10.1021/ci800157j DOI: 10.1021/ci800157j]<br />
<br />
6.'''Nair PC''', Srikanth K, Sobhia ME. "QSAR studies on CCR2 antagonists with chiral sensitive hologram descriptors".<br />
''Bioorg Med Chem Lett.'' 2008 Feb;18(4):1323-30. [http://dx.doi.org/10.1016/j.bmcl.2008.01.023 DOI: 10.1016/j.bmcl.2008.01.023]<br />
<br />
7.Srikanth K, '''Nair PC''', Sobhia ME. "Probing the structural and topological requirements for CCR2 antagonism: holographic QSAR for <br> indolopiperidine derivatives".''Bioorg Med Chem Lett.'' 2008 Feb;18(4):1450-6. [http://dx.doi.org/10.1016/j.bmcl.2007.12.072 DOI: 10.1016/j.bmcl.2007.12.072]<br />
<br />
8.'''Nair PC''', Sobhia ME. "Comparative QSTR studies for predicting mutagenicity of nitro compounds".<br />
''J Mol Graph Model.'' 2008 Feb;26(6):916-34. [http://dx.doi.org/10.1016/j.jmgm.2007.06.006 DOI:10.1016/j.jmgm.2007.06.006]<br />
<br />
9.'''Nair PC''', Sobhia ME. "Quantitative structure activity relationship studies on thiourea analogues as influenza virus neuraminidase inhibitors". ''Eur J Med Chem.'' 2008 Feb;43(2):293-9. [http://dx.doi.org/10.1016/j.ejmech.2007.03.020 DOI: 10.1016/j.ejmech.2007.03.020]<br />
<br />
10.'''Nair PC''', Sobhia ME."CoMFA based de novo design of pyridazine analogs as PTP1B inhibitors".<br />
''J Mol Graph Model.'' 2007 Jul;26(1):117-23. [http://dx.doi.org/10.1016/j.jmgm.2006.10.002 DOI: 10.1016/j.jmgm.2006.10.002]<br />
<br />
11.Khurana J, '''Nair P''',Sobhia ME. "Design of Allosteric Ligands Using Computer Aided Drug Design (CADD) Techniques", Current Research & Information on Pharmaceutical Sciences (CRIPS), 2006 Apr;7(2):8-13.(Review Article)<br><br />
<br />
== Poster Presentations ==<br />
1.'''Nair PC''', Malde AK, Mark AE."Validation of fragment hits in X-ray crystal complexes", The East Coast Protein Meeting, Coffs Harbour NSW, Australia, 15-17th July 2011<br />
<br />
2.'''Nair PC''', Malde AK, Mark AE."The structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-methyltransferase (PNMT): A Molecular Dynamics and Free Energy study", Molecular Modelling 2010, Melbourne, Australia, 28Nov-1Dec 2010.<br />
<br />
3.'''Nair PC''', Malde AK, Mark AE.Investigating structural requirements for PNMT inhibition: A molecular dynamics and free energy calculation study", Division of chemistry and structural biology symposium, Institute of Molecular Bioscience, Brisbane, Australia, Nov 18-19 2010.<br />
<br />
4.'''Nair PC''', Malde AK, Mark AE. "Investigation of ligand interaction and binding free Energy of 1,2,3,4 tetrahydroisoquinoline analogues as PNMT inhibitors", 61st Indian Pharmaceutical Congress, 11-13 December 2009.<br />
<br />
5.'''Nair PC''', Sobhia ME. "Identification of Novel CCR2 Scaffolds Through Fingerprint Directed Virtual Screening", Virtual Discovery Europe (Computer Aided Drug Design and Screening) London, England, 24-25 October 2007. (Presented by Dr. M. Elizabeth Sobhia, NIPER )<br />
<br />
6.'''Nair PC''', Sobhia ME. "Synergistic application of target structure based alignment and 3D-QSAR study of protein tyrosine phosphatases 1B (PTP1B) inhibitors", Workshop on Pharmcoinformatics: Tools for Drug Target Identification, NIPER, India, March 14-16, 2007.<br />
<br />
7.'''Nair PC''', Sobhia ME. "Quantitative Structure Toxicity Relationship (QSTR) Studies for Predicting Mutagenicity of Nitro Compounds", International Conference on Chemoinformatics, NCL, Pune, India, Jan 22, 2007.<br />
<br />
8.'''Nair PC''', Sobhia ME. "Design of novel PTP1B inhibitors using 3D-QSAR and concept of hypothetical cavity generation", Workshop on Pharmacoinformatics: QSAR, NIPER, India, March 3-4, 2006.<br />
<br />
== Other Conferences/Scientific visits ==<br />
<br />
Structural Biology Symposium, Institute for Glycomics, Griffith University, Gold Coast, Australia, 2009. <br />
<br />
Molecular Modelling (MM2009), Gold Coast, Queensland, Australia, July 26-29 2009. <br />
<br />
Attended 8th National Center of Competence in Research (NCCR) Practical Course in the area of computational structural biology, Kandersteg, Switzerland, Jan 10-15 2010.<br />
<br />
Visited as a scientific guest in the laboratory of Prof. Wilfred F. van Gunsteren, ETH Zurich, Switzerland, Jan 16-29 2010.<br />
<br />
== Contact Details ==<br />
<br />
Endeavour IPRS Doctoral Fellow <br><br />
Molecular Dynamics Group <br><br />
School of Chemistry and Molecular Biosciences (SCMB) <br><br />
Molecular Biosciences Building (#76) <br><br />
The University of Queensland <br><br />
St. Lucia Campus, Brisbane, QLD 4072 <br><br />
Australia <br><br />
<br />
'''email''' p.nair@uq.edu.au</div>PramodNairhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Pramod_Nair&diff=15996Pramod Nair2011-10-28T00:58:27Z<p>PramodNair: /* Publications */</p>
<hr />
<div>Automated Force Field Topology Builder (ATB) for GROMOS and GROMACS : MD group of Prof. Alan E. Mark<br />
http://compbio.biosci.uq.edu.au/atb/ <br />
<br />
== Research Interests ==<br />
Computer Aided Drug Design (CADD) and Free Energy Calculations<br />
<br />
Alternate Free energy methods to aid high-throughput virtual screening in drug discovery<br />
<br />
Molecular Dynamics simulations of macromolecular and small molecular systems<br />
<br />
== Academic ==<br />
'''B. Pharm.''' Bombay College of Pharmacy, University of Mumbai, India 2001-2005 <br><br />
'''MS (Pharm.)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2005-2007 <br><br />
'''Junior Research Fellow (JRF)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2007-2008 <br><br />
'''PhD Student''' Molecular Dynamics Group, School of Chemistry and Molecular Biosciences (SCMB),University of Queensland, Australia 2009 <br><br />
<br />
== Publications ==<br />
1. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, '''Nair PC''', Oostenbrink C, Mark AE. An Automated force field Topology Builder (ATB) and repository: version 1.0. ''J Chem Theory Comput.'' 2011, accepted.[http://dx.doi.org/10.1021/ct200196m DOI: 10.1021/ct200196m]<br />
<br />
2. Riniker S, Christ CD, Hansen N, Mark AE, '''Nair PC''', van Gunsteren WF. Comparison of Enveloping Distribution Sampling and Thermodynamic Integration to Calculate Binding Free Energies of Phenylethanolamine N-Methyltransferase Inhibitors. ''J Chem Phys.'' 2011 Jul;135(2):024105-13. [http://dx.doi.org/10.1063/1.3604534 DOI:10.1063/1.3604534]<br />
<br />
3.'''Nair PC''', Malde AK, Mark AE."Using theory to reconcile experiment: the structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-MethylTransferase (PNMT)". ''J Chem Theory Comput.'' 2011, May;7(5):1458-1468. [http://dx.doi.org/10.1021/ct1007229 DOI: 10.1021/ct1007229]<br />
<br />
4.'''Nair PC'''. "Molecular Field Analysis (MFA) and other QSAR techniques in development of phosphatase inhibitors".<br />
''Anticancer Agents Med Chem.'' 2011 Jan;11(1):151-163. (Invited Review Article) [http://dx.doi.org/10.2174/187152011794941181 DOI: 10.2174/187152011794941181]<br />
<br />
5.'''Nair PC''', Sobhia ME. "Fingerprint directed scaffold hopping for identification of CCR2 antagonists".<br />
''J Chem Inf Model.'' 2008 Sep;48(9):1891-902. [http://dx.doi.org/10.1021/ci800157j DOI: 10.1021/ci800157j]<br />
<br />
6.'''Nair PC''', Srikanth K, Sobhia ME. "QSAR studies on CCR2 antagonists with chiral sensitive hologram descriptors".<br />
''Bioorg Med Chem Lett.'' 2008 Feb;18(4):1323-30. [http://dx.doi.org/10.1016/j.bmcl.2008.01.023 DOI: 10.1016/j.bmcl.2008.01.023]<br />
<br />
7.Srikanth K, '''Nair PC''', Sobhia ME. "Probing the structural and topological requirements for CCR2 antagonism: holographic QSAR for <br> indolopiperidine derivatives".''Bioorg Med Chem Lett.'' 2008 Feb;18(4):1450-6. [http://dx.doi.org/10.1016/j.bmcl.2007.12.072 DOI: 10.1016/j.bmcl.2007.12.072]<br />
<br />
8.'''Nair PC''', Sobhia ME. "Comparative QSTR studies for predicting mutagenicity of nitro compounds".<br />
''J Mol Graph Model.'' 2008 Feb;26(6):916-34. [http://dx.doi.org/10.1016/j.jmgm.2007.06.006 DOI:10.1016/j.jmgm.2007.06.006]<br />
<br />
9.'''Nair PC''', Sobhia ME. "Quantitative structure activity relationship studies on thiourea analogues as influenza virus neuraminidase inhibitors". ''Eur J Med Chem.'' 2008 Feb;43(2):293-9. [http://dx.doi.org/10.1016/j.ejmech.2007.03.020 DOI: 10.1016/j.ejmech.2007.03.020]<br />
<br />
10.'''Nair PC''', Sobhia ME."CoMFA based de novo design of pyridazine analogs as PTP1B inhibitors".<br />
''J Mol Graph Model.'' 2007 Jul;26(1):117-23. [http://dx.doi.org/10.1016/j.jmgm.2006.10.002 DOI: 10.1016/j.jmgm.2006.10.002]<br />
<br />
11.Khurana J, '''Nair P''',Sobhia ME. "Design of Allosteric Ligands Using Computer Aided Drug Design (CADD) Techniques", Current Research & Information on Pharmaceutical Sciences (CRIPS), 2006 Apr;7(2):8-13.(Review Article)<br><br />
<br />
== Poster Presentations ==<br />
1.'''Nair PC''', Malde AK, Mark AE."Validation of fragment hits in X-ray crystal complexes", The East Coast Protein Meeting, Coffs Harbour NSW, Australia, 15-17th July 2011<br />
<br />
2.'''Nair PC''', Malde AK, Mark AE."The structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-methyltransferase (PNMT): A Molecular Dynamics and Free Energy study", Molecular Modelling 2010, Melbourne, Australia, 28Nov-1Dec 2010.<br />
<br />
3.'''Nair PC''', Malde AK, Mark AE.Investigating structural requirements for PNMT inhibition: A molecular dynamics and free energy calculation study", Division of chemistry and structural biology symposium, Institute of Molecular Bioscience, Brisbane, Australia, Nov 18-19 2010.<br />
<br />
4.'''Nair PC''', Malde AK, Mark AE. "Investigation of ligand interaction and binding free Energy of 1,2,3,4 tetrahydroisoquinoline analogues as PNMT inhibitors", 61st Indian Pharmaceutical Congress, 11-13 December 2009.<br />
<br />
5.'''Nair PC''', Sobhia ME. "Identification of Novel CCR2 Scaffolds Through Fingerprint Directed Virtual Screening", Virtual Discovery Europe (Computer Aided Drug Design and Screening) London, England, 24-25 October 2007. (Presented by Dr. M. Elizabeth Sobhia, NIPER )<br />
<br />
6.'''Nair PC''', Sobhia ME. "Synergistic application of target structure based alignment and 3D-QSAR study of protein tyrosine phosphatases 1B (PTP1B) inhibitors", Workshop on Pharmcoinformatics: Tools for Drug Target Identification, NIPER, India, March 14-16, 2007.<br />
<br />
7.'''Nair PC''', Sobhia ME. "Quantitative Structure Toxicity Relationship (QSTR) Studies for Predicting Mutagenicity of Nitro Compounds", International Conference on Chemoinformatics, NCL, Pune, India, Jan 22, 2007.<br />
<br />
8.'''Nair PC''', Sobhia ME. "Design of novel PTP1B inhibitors using 3D-QSAR and concept of hypothetical cavity generation", Workshop on Pharmacoinformatics: QSAR, NIPER, India, March 3-4, 2006.<br />
<br />
== Other Conferences/Scientific visits ==<br />
<br />
Structural Biology Symposium, Institute for Glycomics, Griffith University, Gold Coast, Australia, 2009. <br />
<br />
Molecular Modelling (MM2009), Gold Coast, Queensland, Australia, July 26-29 2009. <br />
<br />
Attended 8th National Center of Competence in Research (NCCR) Practical Course in the area of computational structural biology, Kandersteg, Switzerland, Jan 10-15 2010.<br />
<br />
Visited as a scientific guest in the laboratory of Prof. Wilfred F. van Gunsteren, ETH Zurich, Switzerland, Jan 16-29 2010.<br />
<br />
== Contact Details ==<br />
<br />
Endeavour IPRS Doctoral Fellow <br><br />
Molecular Dynamics Group <br><br />
School of Chemistry and Molecular Biosciences (SCMB) <br><br />
Molecular Biosciences Building (#76) <br><br />
The University of Queensland <br><br />
St. Lucia Campus, Brisbane, QLD 4072 <br><br />
Australia <br><br />
<br />
'''email''' p.nair@uq.edu.au</div>PramodNairhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Pramod_Nair&diff=15995Pramod Nair2011-10-28T00:57:48Z<p>PramodNair: /* Publications */</p>
<hr />
<div>Automated Force Field Topology Builder (ATB) for GROMOS and GROMACS : MD group of Prof. Alan E. Mark<br />
http://compbio.biosci.uq.edu.au/atb/ <br />
<br />
== Research Interests ==<br />
Computer Aided Drug Design (CADD) and Free Energy Calculations<br />
<br />
Alternate Free energy methods to aid high-throughput virtual screening in drug discovery<br />
<br />
Molecular Dynamics simulations of macromolecular and small molecular systems<br />
<br />
== Academic ==<br />
'''B. Pharm.''' Bombay College of Pharmacy, University of Mumbai, India 2001-2005 <br><br />
'''MS (Pharm.)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2005-2007 <br><br />
'''Junior Research Fellow (JRF)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2007-2008 <br><br />
'''PhD Student''' Molecular Dynamics Group, School of Chemistry and Molecular Biosciences (SCMB),University of Queensland, Australia 2009 <br><br />
<br />
== Publications ==<br />
1. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, '''Nair PC''', Oostenbrink C, Mark AE. An Automated force field Topology Builder (ATB) and repository: version 1.0. ''J Chem Theory Comput.'' 2011, submitted.[http://dx.doi.org/10.1021/ct200196m DOI: 10.1021/ct200196m]<br />
<br />
2. Riniker S, Christ CD, Hansen N, Mark AE, '''Nair PC''', van Gunsteren WF. Comparison of Enveloping Distribution Sampling and Thermodynamic Integration to Calculate Binding Free Energies of Phenylethanolamine N-Methyltransferase Inhibitors. ''J Chem Phys.'' 2011 Jul;135(2):024105-13. [http://dx.doi.org/10.1063/1.3604534 DOI:10.1063/1.3604534]<br />
<br />
3.'''Nair PC''', Malde AK, Mark AE."Using theory to reconcile experiment: the structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-MethylTransferase (PNMT)". ''J Chem Theory Comput.'' 2011, May;7(5):1458-1468. [http://dx.doi.org/10.1021/ct1007229 DOI: 10.1021/ct1007229]<br />
<br />
4.'''Nair PC'''. "Molecular Field Analysis (MFA) and other QSAR techniques in development of phosphatase inhibitors".<br />
''Anticancer Agents Med Chem.'' 2011 Jan;11(1):151-163. (Invited Review Article) [http://dx.doi.org/10.2174/187152011794941181 DOI: 10.2174/187152011794941181]<br />
<br />
5.'''Nair PC''', Sobhia ME. "Fingerprint directed scaffold hopping for identification of CCR2 antagonists".<br />
''J Chem Inf Model.'' 2008 Sep;48(9):1891-902. [http://dx.doi.org/10.1021/ci800157j DOI: 10.1021/ci800157j]<br />
<br />
6.'''Nair PC''', Srikanth K, Sobhia ME. "QSAR studies on CCR2 antagonists with chiral sensitive hologram descriptors".<br />
''Bioorg Med Chem Lett.'' 2008 Feb;18(4):1323-30. [http://dx.doi.org/10.1016/j.bmcl.2008.01.023 DOI: 10.1016/j.bmcl.2008.01.023]<br />
<br />
7.Srikanth K, '''Nair PC''', Sobhia ME. "Probing the structural and topological requirements for CCR2 antagonism: holographic QSAR for <br> indolopiperidine derivatives".''Bioorg Med Chem Lett.'' 2008 Feb;18(4):1450-6. [http://dx.doi.org/10.1016/j.bmcl.2007.12.072 DOI: 10.1016/j.bmcl.2007.12.072]<br />
<br />
8.'''Nair PC''', Sobhia ME. "Comparative QSTR studies for predicting mutagenicity of nitro compounds".<br />
''J Mol Graph Model.'' 2008 Feb;26(6):916-34. [http://dx.doi.org/10.1016/j.jmgm.2007.06.006 DOI:10.1016/j.jmgm.2007.06.006]<br />
<br />
9.'''Nair PC''', Sobhia ME. "Quantitative structure activity relationship studies on thiourea analogues as influenza virus neuraminidase inhibitors". ''Eur J Med Chem.'' 2008 Feb;43(2):293-9. [http://dx.doi.org/10.1016/j.ejmech.2007.03.020 DOI: 10.1016/j.ejmech.2007.03.020]<br />
<br />
10.'''Nair PC''', Sobhia ME."CoMFA based de novo design of pyridazine analogs as PTP1B inhibitors".<br />
''J Mol Graph Model.'' 2007 Jul;26(1):117-23. [http://dx.doi.org/10.1016/j.jmgm.2006.10.002 DOI: 10.1016/j.jmgm.2006.10.002]<br />
<br />
11.Khurana J, '''Nair P''',Sobhia ME. "Design of Allosteric Ligands Using Computer Aided Drug Design (CADD) Techniques", Current Research & Information on Pharmaceutical Sciences (CRIPS), 2006 Apr;7(2):8-13.(Review Article)<br><br />
<br />
== Poster Presentations ==<br />
1.'''Nair PC''', Malde AK, Mark AE."Validation of fragment hits in X-ray crystal complexes", The East Coast Protein Meeting, Coffs Harbour NSW, Australia, 15-17th July 2011<br />
<br />
2.'''Nair PC''', Malde AK, Mark AE."The structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-methyltransferase (PNMT): A Molecular Dynamics and Free Energy study", Molecular Modelling 2010, Melbourne, Australia, 28Nov-1Dec 2010.<br />
<br />
3.'''Nair PC''', Malde AK, Mark AE.Investigating structural requirements for PNMT inhibition: A molecular dynamics and free energy calculation study", Division of chemistry and structural biology symposium, Institute of Molecular Bioscience, Brisbane, Australia, Nov 18-19 2010.<br />
<br />
4.'''Nair PC''', Malde AK, Mark AE. "Investigation of ligand interaction and binding free Energy of 1,2,3,4 tetrahydroisoquinoline analogues as PNMT inhibitors", 61st Indian Pharmaceutical Congress, 11-13 December 2009.<br />
<br />
5.'''Nair PC''', Sobhia ME. "Identification of Novel CCR2 Scaffolds Through Fingerprint Directed Virtual Screening", Virtual Discovery Europe (Computer Aided Drug Design and Screening) London, England, 24-25 October 2007. (Presented by Dr. M. Elizabeth Sobhia, NIPER )<br />
<br />
6.'''Nair PC''', Sobhia ME. "Synergistic application of target structure based alignment and 3D-QSAR study of protein tyrosine phosphatases 1B (PTP1B) inhibitors", Workshop on Pharmcoinformatics: Tools for Drug Target Identification, NIPER, India, March 14-16, 2007.<br />
<br />
7.'''Nair PC''', Sobhia ME. "Quantitative Structure Toxicity Relationship (QSTR) Studies for Predicting Mutagenicity of Nitro Compounds", International Conference on Chemoinformatics, NCL, Pune, India, Jan 22, 2007.<br />
<br />
8.'''Nair PC''', Sobhia ME. "Design of novel PTP1B inhibitors using 3D-QSAR and concept of hypothetical cavity generation", Workshop on Pharmacoinformatics: QSAR, NIPER, India, March 3-4, 2006.<br />
<br />
== Other Conferences/Scientific visits ==<br />
<br />
Structural Biology Symposium, Institute for Glycomics, Griffith University, Gold Coast, Australia, 2009. <br />
<br />
Molecular Modelling (MM2009), Gold Coast, Queensland, Australia, July 26-29 2009. <br />
<br />
Attended 8th National Center of Competence in Research (NCCR) Practical Course in the area of computational structural biology, Kandersteg, Switzerland, Jan 10-15 2010.<br />
<br />
Visited as a scientific guest in the laboratory of Prof. Wilfred F. van Gunsteren, ETH Zurich, Switzerland, Jan 16-29 2010.<br />
<br />
== Contact Details ==<br />
<br />
Endeavour IPRS Doctoral Fellow <br><br />
Molecular Dynamics Group <br><br />
School of Chemistry and Molecular Biosciences (SCMB) <br><br />
Molecular Biosciences Building (#76) <br><br />
The University of Queensland <br><br />
St. Lucia Campus, Brisbane, QLD 4072 <br><br />
Australia <br><br />
<br />
'''email''' p.nair@uq.edu.au</div>PramodNairhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Pramod_Nair&diff=15971Pramod Nair2011-08-31T04:12:36Z<p>PramodNair: /* Publications */</p>
<hr />
<div>Automated Force Field Topology Builder (ATB) for GROMOS and GROMACS : MD group of Prof. Alan E. Mark<br />
http://compbio.biosci.uq.edu.au/atb/ <br />
<br />
== Research Interests ==<br />
Computer Aided Drug Design (CADD) and Free Energy Calculations<br />
<br />
Alternate Free energy methods to aid high-throughput virtual screening in drug discovery<br />
<br />
Molecular Dynamics simulations of macromolecular and small molecular systems<br />
<br />
== Academic ==<br />
'''B. Pharm.''' Bombay College of Pharmacy, University of Mumbai, India 2001-2005 <br><br />
'''MS (Pharm.)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2005-2007 <br><br />
'''Junior Research Fellow (JRF)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2007-2008 <br><br />
'''PhD Student''' Molecular Dynamics Group, School of Chemistry and Molecular Biosciences (SCMB),University of Queensland, Australia 2009 <br><br />
<br />
== Publications ==<br />
1. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, '''Nair PC''', Oostenbrink C, Mark AE. An Automated force field Topology Builder (ATB) and repository: version 1.0. ''J Chem Theory Comput.'' 2011, submitted.<br />
<br />
2. Riniker S, Christ CD, Hansen N, Mark AE, '''Nair PC''', van Gunsteren WF. Comparison of Enveloping Distribution Sampling and Thermodynamic Integration to Calculate Binding Free Energies of Phenylethanolamine N-Methyltransferase Inhibitors. ''J Chem Phys.'' 2011 Jul;135(2):024105-13. [http://dx.doi.org/10.1063/1.3604534 DOI:10.1063/1.3604534]<br />
<br />
3.'''Nair PC''', Malde AK, Mark AE."Using theory to reconcile experiment: the structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-MethylTransferase (PNMT)". ''J Chem Theory Comput.'' 2011, May;7(5):1458-1468. [http://dx.doi.org/10.1021/ct1007229 DOI: 10.1021/ct1007229]<br />
<br />
4.'''Nair PC'''. "Molecular Field Analysis (MFA) and other QSAR techniques in development of phosphatase inhibitors".<br />
''Anticancer Agents Med Chem.'' 2011 Jan;11(1):151-163. (Invited Review Article) [http://dx.doi.org/10.2174/187152011794941181 DOI: 10.2174/187152011794941181]<br />
<br />
5.'''Nair PC''', Sobhia ME. "Fingerprint directed scaffold hopping for identification of CCR2 antagonists".<br />
''J Chem Inf Model.'' 2008 Sep;48(9):1891-902. [http://dx.doi.org/10.1021/ci800157j DOI: 10.1021/ci800157j]<br />
<br />
6.'''Nair PC''', Srikanth K, Sobhia ME. "QSAR studies on CCR2 antagonists with chiral sensitive hologram descriptors".<br />
''Bioorg Med Chem Lett.'' 2008 Feb;18(4):1323-30. [http://dx.doi.org/10.1016/j.bmcl.2008.01.023 DOI: 10.1016/j.bmcl.2008.01.023]<br />
<br />
7.Srikanth K, '''Nair PC''', Sobhia ME. "Probing the structural and topological requirements for CCR2 antagonism: holographic QSAR for <br> indolopiperidine derivatives".''Bioorg Med Chem Lett.'' 2008 Feb;18(4):1450-6. [http://dx.doi.org/10.1016/j.bmcl.2007.12.072 DOI: 10.1016/j.bmcl.2007.12.072]<br />
<br />
8.'''Nair PC''', Sobhia ME. "Comparative QSTR studies for predicting mutagenicity of nitro compounds".<br />
''J Mol Graph Model.'' 2008 Feb;26(6):916-34. [http://dx.doi.org/10.1016/j.jmgm.2007.06.006 DOI:10.1016/j.jmgm.2007.06.006]<br />
<br />
9.'''Nair PC''', Sobhia ME. "Quantitative structure activity relationship studies on thiourea analogues as influenza virus neuraminidase inhibitors". ''Eur J Med Chem.'' 2008 Feb;43(2):293-9. [http://dx.doi.org/10.1016/j.ejmech.2007.03.020 DOI: 10.1016/j.ejmech.2007.03.020]<br />
<br />
10.'''Nair PC''', Sobhia ME."CoMFA based de novo design of pyridazine analogs as PTP1B inhibitors".<br />
''J Mol Graph Model.'' 2007 Jul;26(1):117-23. [http://dx.doi.org/10.1016/j.jmgm.2006.10.002 DOI: 10.1016/j.jmgm.2006.10.002]<br />
<br />
11.Khurana J, '''Nair P''',Sobhia ME. "Design of Allosteric Ligands Using Computer Aided Drug Design (CADD) Techniques", Current Research & Information on Pharmaceutical Sciences (CRIPS), 2006 Apr;7(2):8-13.(Review Article)<br><br />
<br />
== Poster Presentations ==<br />
1.'''Nair PC''', Malde AK, Mark AE."Validation of fragment hits in X-ray crystal complexes", The East Coast Protein Meeting, Coffs Harbour NSW, Australia, 15-17th July 2011<br />
<br />
2.'''Nair PC''', Malde AK, Mark AE."The structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-methyltransferase (PNMT): A Molecular Dynamics and Free Energy study", Molecular Modelling 2010, Melbourne, Australia, 28Nov-1Dec 2010.<br />
<br />
3.'''Nair PC''', Malde AK, Mark AE.Investigating structural requirements for PNMT inhibition: A molecular dynamics and free energy calculation study", Division of chemistry and structural biology symposium, Institute of Molecular Bioscience, Brisbane, Australia, Nov 18-19 2010.<br />
<br />
4.'''Nair PC''', Malde AK, Mark AE. "Investigation of ligand interaction and binding free Energy of 1,2,3,4 tetrahydroisoquinoline analogues as PNMT inhibitors", 61st Indian Pharmaceutical Congress, 11-13 December 2009.<br />
<br />
5.'''Nair PC''', Sobhia ME. "Identification of Novel CCR2 Scaffolds Through Fingerprint Directed Virtual Screening", Virtual Discovery Europe (Computer Aided Drug Design and Screening) London, England, 24-25 October 2007. (Presented by Dr. M. Elizabeth Sobhia, NIPER )<br />
<br />
6.'''Nair PC''', Sobhia ME. "Synergistic application of target structure based alignment and 3D-QSAR study of protein tyrosine phosphatases 1B (PTP1B) inhibitors", Workshop on Pharmcoinformatics: Tools for Drug Target Identification, NIPER, India, March 14-16, 2007.<br />
<br />
7.'''Nair PC''', Sobhia ME. "Quantitative Structure Toxicity Relationship (QSTR) Studies for Predicting Mutagenicity of Nitro Compounds", International Conference on Chemoinformatics, NCL, Pune, India, Jan 22, 2007.<br />
<br />
8.'''Nair PC''', Sobhia ME. "Design of novel PTP1B inhibitors using 3D-QSAR and concept of hypothetical cavity generation", Workshop on Pharmacoinformatics: QSAR, NIPER, India, March 3-4, 2006.<br />
<br />
== Other Conferences/Scientific visits ==<br />
<br />
Structural Biology Symposium, Institute for Glycomics, Griffith University, Gold Coast, Australia, 2009. <br />
<br />
Molecular Modelling (MM2009), Gold Coast, Queensland, Australia, July 26-29 2009. <br />
<br />
Attended 8th National Center of Competence in Research (NCCR) Practical Course in the area of computational structural biology, Kandersteg, Switzerland, Jan 10-15 2010.<br />
<br />
Visited as a scientific guest in the laboratory of Prof. Wilfred F. van Gunsteren, ETH Zurich, Switzerland, Jan 16-29 2010.<br />
<br />
== Contact Details ==<br />
<br />
Endeavour IPRS Doctoral Fellow <br><br />
Molecular Dynamics Group <br><br />
School of Chemistry and Molecular Biosciences (SCMB) <br><br />
Molecular Biosciences Building (#76) <br><br />
The University of Queensland <br><br />
St. Lucia Campus, Brisbane, QLD 4072 <br><br />
Australia <br><br />
<br />
'''email''' p.nair@uq.edu.au</div>PramodNairhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Pramod_Nair&diff=15970Pramod Nair2011-08-31T04:11:01Z<p>PramodNair: /* Publications */</p>
<hr />
<div>Automated Force Field Topology Builder (ATB) for GROMOS and GROMACS : MD group of Prof. Alan E. Mark<br />
http://compbio.biosci.uq.edu.au/atb/ <br />
<br />
== Research Interests ==<br />
Computer Aided Drug Design (CADD) and Free Energy Calculations<br />
<br />
Alternate Free energy methods to aid high-throughput virtual screening in drug discovery<br />
<br />
Molecular Dynamics simulations of macromolecular and small molecular systems<br />
<br />
== Academic ==<br />
'''B. Pharm.''' Bombay College of Pharmacy, University of Mumbai, India 2001-2005 <br><br />
'''MS (Pharm.)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2005-2007 <br><br />
'''Junior Research Fellow (JRF)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2007-2008 <br><br />
'''PhD Student''' Molecular Dynamics Group, School of Chemistry and Molecular Biosciences (SCMB),University of Queensland, Australia 2009 <br><br />
<br />
== Publications ==<br />
1. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, '''Nair PC''', Oostenbrink C, Mark AE. An Automated force field Topology Builder (ATB) and repository: version 1.0. ''J Chem Theory Comput.'' 2011, submitted.<br />
<br />
2. Riniker S, Christ CD, Hansen N, Mark AE, '''Nair PC''', van Gunsteren WF. Comparison of Enveloping Distribution Sampling and Thermodynamic Integration to Calculate Binding Free Energies of Phenylethanolamine N-Methyltransferase Inhibitors. ''J Chem Phys.'' 2011 Jul;135(2):024105-13 [http://dx.doi.org/10.1063/1.3604534 DOI:10.1063/1.3604534]<br />
<br />
3.'''Nair PC''', Malde AK, Mark AE."Using theory to reconcile experiment: the structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-MethylTransferase (PNMT)". ''J Chem Theory Comput.'' 2011, May;7(5):1458-1468 <br> [http://dx.doi.org/10.1021/ct1007229 DOI: 10.1021/ct1007229]<br />
<br />
4.'''Nair PC'''. "Molecular Field Analysis (MFA) and other QSAR techniques in development of phosphatase inhibitors".<br />
''Anticancer Agents Med Chem.'' 2011 Jan;11(1):151-163. (Invited Review Article) <br> [http://dx.doi.org/10.2174/187152011794941181 DOI: 10.2174/187152011794941181]<br />
<br />
5.'''Nair PC''', Sobhia ME. "Fingerprint directed scaffold hopping for identification of CCR2 antagonists".<br />
''J Chem Inf Model.'' 2008 Sep;48(9):1891-902. <br> [http://dx.doi.org/10.1021/ci800157j DOI: 10.1021/ci800157j]<br />
<br />
6.'''Nair PC''', Srikanth K, Sobhia ME. "QSAR studies on CCR2 antagonists with chiral sensitive hologram descriptors".<br />
''Bioorg Med Chem Lett.'' 2008 Feb;18(4):1323-30. <br> [http://dx.doi.org/10.1016/j.bmcl.2008.01.023 DOI: 10.1016/j.bmcl.2008.01.023]<br />
<br />
7.Srikanth K, '''Nair PC''', Sobhia ME. "Probing the structural and topological requirements for CCR2 antagonism: holographic QSAR for <br> indolopiperidine derivatives".''Bioorg Med Chem Lett.'' 2008 Feb;18(4):1450-6. <br> <br />
[http://dx.doi.org/10.1016/j.bmcl.2007.12.072 DOI: 10.1016/j.bmcl.2007.12.072]<br />
<br />
8.'''Nair PC''', Sobhia ME. "Comparative QSTR studies for predicting mutagenicity of nitro compounds".<br />
''J Mol Graph Model.'' 2008 Feb;26(6):916-34. <br> [http://dx.doi.org/10.1016/j.jmgm.2007.06.006 DOI:10.1016/j.jmgm.2007.06.006]<br />
<br />
9.'''Nair PC''', Sobhia ME. "Quantitative structure activity relationship studies on thiourea analogues as influenza virus neuraminidase inhibitors". ''Eur J Med Chem.'' 2008 Feb;43(2):293-9. <br> <br />
[http://dx.doi.org/10.1016/j.ejmech.2007.03.020 DOI: 10.1016/j.ejmech.2007.03.020]<br />
<br />
10.'''Nair PC''', Sobhia ME."CoMFA based de novo design of pyridazine analogs as PTP1B inhibitors".<br />
''J Mol Graph Model.'' 2007 Jul;26(1):117-23. <br> <br />
[http://dx.doi.org/10.1016/j.jmgm.2006.10.002 DOI: 10.1016/j.jmgm.2006.10.002]<br />
<br />
11.Khurana J, '''Nair P''',Sobhia ME. "Design of Allosteric Ligands Using Computer Aided Drug Design (CADD) Techniques", Current Research & Information on Pharmaceutical Sciences (CRIPS), 2006 Apr;7(2):8-13.(Review Article)<br><br />
<br />
== Poster Presentations ==<br />
1.'''Nair PC''', Malde AK, Mark AE."Validation of fragment hits in X-ray crystal complexes", The East Coast Protein Meeting, Coffs Harbour NSW, Australia, 15-17th July 2011<br />
<br />
2.'''Nair PC''', Malde AK, Mark AE."The structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-methyltransferase (PNMT): A Molecular Dynamics and Free Energy study", Molecular Modelling 2010, Melbourne, Australia, 28Nov-1Dec 2010.<br />
<br />
3.'''Nair PC''', Malde AK, Mark AE.Investigating structural requirements for PNMT inhibition: A molecular dynamics and free energy calculation study", Division of chemistry and structural biology symposium, Institute of Molecular Bioscience, Brisbane, Australia, Nov 18-19 2010.<br />
<br />
4.'''Nair PC''', Malde AK, Mark AE. "Investigation of ligand interaction and binding free Energy of 1,2,3,4 tetrahydroisoquinoline analogues as PNMT inhibitors", 61st Indian Pharmaceutical Congress, 11-13 December 2009.<br />
<br />
5.'''Nair PC''', Sobhia ME. "Identification of Novel CCR2 Scaffolds Through Fingerprint Directed Virtual Screening", Virtual Discovery Europe (Computer Aided Drug Design and Screening) London, England, 24-25 October 2007. (Presented by Dr. M. Elizabeth Sobhia, NIPER )<br />
<br />
6.'''Nair PC''', Sobhia ME. "Synergistic application of target structure based alignment and 3D-QSAR study of protein tyrosine phosphatases 1B (PTP1B) inhibitors", Workshop on Pharmcoinformatics: Tools for Drug Target Identification, NIPER, India, March 14-16, 2007.<br />
<br />
7.'''Nair PC''', Sobhia ME. "Quantitative Structure Toxicity Relationship (QSTR) Studies for Predicting Mutagenicity of Nitro Compounds", International Conference on Chemoinformatics, NCL, Pune, India, Jan 22, 2007.<br />
<br />
8.'''Nair PC''', Sobhia ME. "Design of novel PTP1B inhibitors using 3D-QSAR and concept of hypothetical cavity generation", Workshop on Pharmacoinformatics: QSAR, NIPER, India, March 3-4, 2006.<br />
<br />
== Other Conferences/Scientific visits ==<br />
<br />
Structural Biology Symposium, Institute for Glycomics, Griffith University, Gold Coast, Australia, 2009. <br />
<br />
Molecular Modelling (MM2009), Gold Coast, Queensland, Australia, July 26-29 2009. <br />
<br />
Attended 8th National Center of Competence in Research (NCCR) Practical Course in the area of computational structural biology, Kandersteg, Switzerland, Jan 10-15 2010.<br />
<br />
Visited as a scientific guest in the laboratory of Prof. Wilfred F. van Gunsteren, ETH Zurich, Switzerland, Jan 16-29 2010.<br />
<br />
== Contact Details ==<br />
<br />
Endeavour IPRS Doctoral Fellow <br><br />
Molecular Dynamics Group <br><br />
School of Chemistry and Molecular Biosciences (SCMB) <br><br />
Molecular Biosciences Building (#76) <br><br />
The University of Queensland <br><br />
St. Lucia Campus, Brisbane, QLD 4072 <br><br />
Australia <br><br />
<br />
'''email''' p.nair@uq.edu.au</div>PramodNairhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Pramod_Nair&diff=15969Pramod Nair2011-08-31T04:10:09Z<p>PramodNair: /* Publications */</p>
<hr />
<div>Automated Force Field Topology Builder (ATB) for GROMOS and GROMACS : MD group of Prof. Alan E. Mark<br />
http://compbio.biosci.uq.edu.au/atb/ <br />
<br />
== Research Interests ==<br />
Computer Aided Drug Design (CADD) and Free Energy Calculations<br />
<br />
Alternate Free energy methods to aid high-throughput virtual screening in drug discovery<br />
<br />
Molecular Dynamics simulations of macromolecular and small molecular systems<br />
<br />
== Academic ==<br />
'''B. Pharm.''' Bombay College of Pharmacy, University of Mumbai, India 2001-2005 <br><br />
'''MS (Pharm.)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2005-2007 <br><br />
'''Junior Research Fellow (JRF)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2007-2008 <br><br />
'''PhD Student''' Molecular Dynamics Group, School of Chemistry and Molecular Biosciences (SCMB),University of Queensland, Australia 2009 <br><br />
<br />
== Publications ==<br />
1. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, '''Nair PC''', Oostenbrink C, Mark AE. An Automated force field Topology Builder (ATB) and repository: version 1.0. ''J Chem Theory Comput.'' 2011, submitted.<br />
<br />
2. Riniker S, Christ CD, Hansen N, Mark AE, '''Nair PC''', van Gunsteren WF. Comparison of Enveloping Distribution Sampling and Thermodynamic Integration to Calculate Binding Free Energies of Phenylethanolamine N-Methyltransferase Inhibitors. ''J Chem Phys.'' 2011 Jul;135(2):024105-13 <br> [http://dx.doi.org/10.1063/1.3604534 DOI:10.1063/1.3604534]<br />
<br />
3.'''Nair PC''', Malde AK, Mark AE."Using theory to reconcile experiment: the structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-MethylTransferase (PNMT)". ''J Chem Theory Comput.'' 2011, May;7(5):1458-1468 <br> [http://dx.doi.org/10.1021/ct1007229 DOI: 10.1021/ct1007229]<br />
<br />
4.'''Nair PC'''. "Molecular Field Analysis (MFA) and other QSAR techniques in development of phosphatase inhibitors".<br />
''Anticancer Agents Med Chem.'' 2011 Jan;11(1):151-163. (Invited Review Article) <br> [http://dx.doi.org/10.2174/187152011794941181 DOI: 10.2174/187152011794941181]<br />
<br />
5.'''Nair PC''', Sobhia ME. "Fingerprint directed scaffold hopping for identification of CCR2 antagonists".<br />
''J Chem Inf Model.'' 2008 Sep;48(9):1891-902. <br> [http://dx.doi.org/10.1021/ci800157j DOI: 10.1021/ci800157j]<br />
<br />
6.'''Nair PC''', Srikanth K, Sobhia ME. "QSAR studies on CCR2 antagonists with chiral sensitive hologram descriptors".<br />
''Bioorg Med Chem Lett.'' 2008 Feb;18(4):1323-30. <br> [http://dx.doi.org/10.1016/j.bmcl.2008.01.023 DOI: 10.1016/j.bmcl.2008.01.023]<br />
<br />
7.Srikanth K, '''Nair PC''', Sobhia ME. "Probing the structural and topological requirements for CCR2 antagonism: holographic QSAR for <br> indolopiperidine derivatives".''Bioorg Med Chem Lett.'' 2008 Feb;18(4):1450-6. <br> <br />
[http://dx.doi.org/10.1016/j.bmcl.2007.12.072 DOI: 10.1016/j.bmcl.2007.12.072]<br />
<br />
8.'''Nair PC''', Sobhia ME. "Comparative QSTR studies for predicting mutagenicity of nitro compounds".<br />
''J Mol Graph Model.'' 2008 Feb;26(6):916-34. <br> [http://dx.doi.org/10.1016/j.jmgm.2007.06.006 DOI:10.1016/j.jmgm.2007.06.006]<br />
<br />
9.'''Nair PC''', Sobhia ME. "Quantitative structure activity relationship studies on thiourea analogues as influenza virus neuraminidase inhibitors". ''Eur J Med Chem.'' 2008 Feb;43(2):293-9. <br> <br />
[http://dx.doi.org/10.1016/j.ejmech.2007.03.020 DOI: 10.1016/j.ejmech.2007.03.020]<br />
<br />
10.'''Nair PC''', Sobhia ME."CoMFA based de novo design of pyridazine analogs as PTP1B inhibitors".<br />
''J Mol Graph Model.'' 2007 Jul;26(1):117-23. <br> <br />
[http://dx.doi.org/10.1016/j.jmgm.2006.10.002 DOI: 10.1016/j.jmgm.2006.10.002]<br />
<br />
11.Khurana J, '''Nair P''',Sobhia ME. "Design of Allosteric Ligands Using Computer Aided Drug Design (CADD) Techniques", Current Research & Information on Pharmaceutical Sciences (CRIPS), 2006 Apr;7(2):8-13.(Review Article)<br><br />
<br />
== Poster Presentations ==<br />
1.'''Nair PC''', Malde AK, Mark AE."Validation of fragment hits in X-ray crystal complexes", The East Coast Protein Meeting, Coffs Harbour NSW, Australia, 15-17th July 2011<br />
<br />
2.'''Nair PC''', Malde AK, Mark AE."The structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-methyltransferase (PNMT): A Molecular Dynamics and Free Energy study", Molecular Modelling 2010, Melbourne, Australia, 28Nov-1Dec 2010.<br />
<br />
3.'''Nair PC''', Malde AK, Mark AE.Investigating structural requirements for PNMT inhibition: A molecular dynamics and free energy calculation study", Division of chemistry and structural biology symposium, Institute of Molecular Bioscience, Brisbane, Australia, Nov 18-19 2010.<br />
<br />
4.'''Nair PC''', Malde AK, Mark AE. "Investigation of ligand interaction and binding free Energy of 1,2,3,4 tetrahydroisoquinoline analogues as PNMT inhibitors", 61st Indian Pharmaceutical Congress, 11-13 December 2009.<br />
<br />
5.'''Nair PC''', Sobhia ME. "Identification of Novel CCR2 Scaffolds Through Fingerprint Directed Virtual Screening", Virtual Discovery Europe (Computer Aided Drug Design and Screening) London, England, 24-25 October 2007. (Presented by Dr. M. Elizabeth Sobhia, NIPER )<br />
<br />
6.'''Nair PC''', Sobhia ME. "Synergistic application of target structure based alignment and 3D-QSAR study of protein tyrosine phosphatases 1B (PTP1B) inhibitors", Workshop on Pharmcoinformatics: Tools for Drug Target Identification, NIPER, India, March 14-16, 2007.<br />
<br />
7.'''Nair PC''', Sobhia ME. "Quantitative Structure Toxicity Relationship (QSTR) Studies for Predicting Mutagenicity of Nitro Compounds", International Conference on Chemoinformatics, NCL, Pune, India, Jan 22, 2007.<br />
<br />
8.'''Nair PC''', Sobhia ME. "Design of novel PTP1B inhibitors using 3D-QSAR and concept of hypothetical cavity generation", Workshop on Pharmacoinformatics: QSAR, NIPER, India, March 3-4, 2006.<br />
<br />
== Other Conferences/Scientific visits ==<br />
<br />
Structural Biology Symposium, Institute for Glycomics, Griffith University, Gold Coast, Australia, 2009. <br />
<br />
Molecular Modelling (MM2009), Gold Coast, Queensland, Australia, July 26-29 2009. <br />
<br />
Attended 8th National Center of Competence in Research (NCCR) Practical Course in the area of computational structural biology, Kandersteg, Switzerland, Jan 10-15 2010.<br />
<br />
Visited as a scientific guest in the laboratory of Prof. Wilfred F. van Gunsteren, ETH Zurich, Switzerland, Jan 16-29 2010.<br />
<br />
== Contact Details ==<br />
<br />
Endeavour IPRS Doctoral Fellow <br><br />
Molecular Dynamics Group <br><br />
School of Chemistry and Molecular Biosciences (SCMB) <br><br />
Molecular Biosciences Building (#76) <br><br />
The University of Queensland <br><br />
St. Lucia Campus, Brisbane, QLD 4072 <br><br />
Australia <br><br />
<br />
'''email''' p.nair@uq.edu.au</div>PramodNairhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Pramod_Nair&diff=15968Pramod Nair2011-08-31T04:00:06Z<p>PramodNair: /* Publications */</p>
<hr />
<div>Automated Force Field Topology Builder (ATB) for GROMOS and GROMACS : MD group of Prof. Alan E. Mark<br />
http://compbio.biosci.uq.edu.au/atb/ <br />
<br />
== Research Interests ==<br />
Computer Aided Drug Design (CADD) and Free Energy Calculations<br />
<br />
Alternate Free energy methods to aid high-throughput virtual screening in drug discovery<br />
<br />
Molecular Dynamics simulations of macromolecular and small molecular systems<br />
<br />
== Academic ==<br />
'''B. Pharm.''' Bombay College of Pharmacy, University of Mumbai, India 2001-2005 <br><br />
'''MS (Pharm.)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2005-2007 <br><br />
'''Junior Research Fellow (JRF)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2007-2008 <br><br />
'''PhD Student''' Molecular Dynamics Group, School of Chemistry and Molecular Biosciences (SCMB),University of Queensland, Australia 2009 <br><br />
<br />
== Publications ==<br />
1. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, '''Nair PC''', Oostenbrink C, Mark AE. An Automated force field Topology Builder (ATB) and repository: version 1.0. ''J Chem Theory Comput.'' 2011, submitted.<br />
<br />
2. Riniker S, Christ CD, Hansen N, Mark AE, '''Nair PC''', van Gunsteren WF. Comparison of Enveloping Distribution Sampling and Thermodynamic Integration to Calculate Binding Free Energies of Phenylethanolamine N-Methyltransferase Inhibitors. ''J Chem Phys.'' 2011 Jul;135(2):024105-13 <br> [http://dx.doi.org/10.1063/1.3604534 DOI:10.1063/1.3604534]<br />
<br />
3.'''Nair PC''', Malde AK, Mark AE."Using theory to reconcile experiment: the structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-MethylTransferase (PNMT)". ''J Chem Theory Comput.'' 2011, May;7(5):1458-1468 <br> [http://dx.doi.org/10.1021/ct1007229 DOI: 10.1021/ct1007229]<br />
<br />
4.'''Nair PC'''. "Molecular Field Analysis (MFA) and other QSAR techniques in development of phosphatase inhibitors".<br />
''Anticancer Agents Med Chem.'' 2011 Jan;11(1):151-163. (Invited Review Article) <br> [http://dx.doi.org/10.2174/187152011794941181 DOI: 10.2174/187152011794941181]<br />
<br />
5.'''Nair PC''', Sobhia ME. "Fingerprint directed scaffold hopping for identification of CCR2 antagonists".<br />
''J Chem Inf Model.'' 2008 Sep;48(9):1891-902. <br> [http://dx.doi.org/10.1021/ci800157j DOI: 10.1021/ci800157j]<br />
<br />
6.'''Nair PC''', Srikanth K, Sobhia ME. "QSAR studies on CCR2 antagonists with chiral sensitive hologram descriptors".<br />
''Bioorg Med Chem Lett.'' 2008 Feb;18(4):1323-30. <br> [http://dx.doi.org/10.1016/j.bmcl.2008.01.023 DOI: 10.1016/j.bmcl.2008.01.023]<br />
<br />
7.Srikanth K, '''Nair PC''', Sobhia ME. "Probing the structural and topological requirements for CCR2 antagonism: holographic QSAR for <br> indolopiperidine derivatives".''Bioorg Med Chem Lett.'' 2008 Feb;18(4):1450-6. <br><br />
<br />
8.'''Nair PC''', Sobhia ME. "Comparative QSTR studies for predicting mutagenicity of nitro compounds".<br />
''J Mol Graph Model.'' 2008 Feb;26(6):916-34. <br><br />
<br />
9.'''Nair PC''', Sobhia ME. "Quantitative structure activity relationship studies on thiourea analogues as influenza virus neuraminidase inhibitors". ''Eur J Med Chem.'' 2008 Feb;43(2):293-9. <br><br />
<br />
10.'''Nair PC''', Sobhia ME."CoMFA based de novo design of pyridazine analogs as PTP1B inhibitors".<br />
''J Mol Graph Model.'' 2007 Jul;26(1):117-23. <br><br />
<br />
11.Khurana J, '''Nair P''',Sobhia ME. "Design of Allosteric Ligands Using Computer Aided Drug Design (CADD) Techniques", Current Research & Information on Pharmaceutical Sciences (CRIPS), 2006 Apr;7(2):8-13.(Review Article)<br><br />
<br />
== Poster Presentations ==<br />
1.'''Nair PC''', Malde AK, Mark AE."Validation of fragment hits in X-ray crystal complexes", The East Coast Protein Meeting, Coffs Harbour NSW, Australia, 15-17th July 2011<br />
<br />
2.'''Nair PC''', Malde AK, Mark AE."The structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-methyltransferase (PNMT): A Molecular Dynamics and Free Energy study", Molecular Modelling 2010, Melbourne, Australia, 28Nov-1Dec 2010.<br />
<br />
3.'''Nair PC''', Malde AK, Mark AE.Investigating structural requirements for PNMT inhibition: A molecular dynamics and free energy calculation study", Division of chemistry and structural biology symposium, Institute of Molecular Bioscience, Brisbane, Australia, Nov 18-19 2010.<br />
<br />
4.'''Nair PC''', Malde AK, Mark AE. "Investigation of ligand interaction and binding free Energy of 1,2,3,4 tetrahydroisoquinoline analogues as PNMT inhibitors", 61st Indian Pharmaceutical Congress, 11-13 December 2009.<br />
<br />
5.'''Nair PC''', Sobhia ME. "Identification of Novel CCR2 Scaffolds Through Fingerprint Directed Virtual Screening", Virtual Discovery Europe (Computer Aided Drug Design and Screening) London, England, 24-25 October 2007. (Presented by Dr. M. Elizabeth Sobhia, NIPER )<br />
<br />
6.'''Nair PC''', Sobhia ME. "Synergistic application of target structure based alignment and 3D-QSAR study of protein tyrosine phosphatases 1B (PTP1B) inhibitors", Workshop on Pharmcoinformatics: Tools for Drug Target Identification, NIPER, India, March 14-16, 2007.<br />
<br />
7.'''Nair PC''', Sobhia ME. "Quantitative Structure Toxicity Relationship (QSTR) Studies for Predicting Mutagenicity of Nitro Compounds", International Conference on Chemoinformatics, NCL, Pune, India, Jan 22, 2007.<br />
<br />
8.'''Nair PC''', Sobhia ME. "Design of novel PTP1B inhibitors using 3D-QSAR and concept of hypothetical cavity generation", Workshop on Pharmacoinformatics: QSAR, NIPER, India, March 3-4, 2006.<br />
<br />
== Other Conferences/Scientific visits ==<br />
<br />
Structural Biology Symposium, Institute for Glycomics, Griffith University, Gold Coast, Australia, 2009. <br />
<br />
Molecular Modelling (MM2009), Gold Coast, Queensland, Australia, July 26-29 2009. <br />
<br />
Attended 8th National Center of Competence in Research (NCCR) Practical Course in the area of computational structural biology, Kandersteg, Switzerland, Jan 10-15 2010.<br />
<br />
Visited as a scientific guest in the laboratory of Prof. Wilfred F. van Gunsteren, ETH Zurich, Switzerland, Jan 16-29 2010.<br />
<br />
== Contact Details ==<br />
<br />
Endeavour IPRS Doctoral Fellow <br><br />
Molecular Dynamics Group <br><br />
School of Chemistry and Molecular Biosciences (SCMB) <br><br />
Molecular Biosciences Building (#76) <br><br />
The University of Queensland <br><br />
St. Lucia Campus, Brisbane, QLD 4072 <br><br />
Australia <br><br />
<br />
'''email''' p.nair@uq.edu.au</div>PramodNairhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Pramod_Nair&diff=15967Pramod Nair2011-08-31T03:59:15Z<p>PramodNair: /* Publications */</p>
<hr />
<div>Automated Force Field Topology Builder (ATB) for GROMOS and GROMACS : MD group of Prof. Alan E. Mark<br />
http://compbio.biosci.uq.edu.au/atb/ <br />
<br />
== Research Interests ==<br />
Computer Aided Drug Design (CADD) and Free Energy Calculations<br />
<br />
Alternate Free energy methods to aid high-throughput virtual screening in drug discovery<br />
<br />
Molecular Dynamics simulations of macromolecular and small molecular systems<br />
<br />
== Academic ==<br />
'''B. Pharm.''' Bombay College of Pharmacy, University of Mumbai, India 2001-2005 <br><br />
'''MS (Pharm.)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2005-2007 <br><br />
'''Junior Research Fellow (JRF)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2007-2008 <br><br />
'''PhD Student''' Molecular Dynamics Group, School of Chemistry and Molecular Biosciences (SCMB),University of Queensland, Australia 2009 <br><br />
<br />
== Publications ==<br />
1. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, '''Nair PC''', Oostenbrink C, Mark AE. An Automated force field Topology Builder (ATB) and repository: version 1.0. ''J Chem Theory Comput.'' 2011, submitted.<br />
<br />
2. Riniker S, Christ CD, Hansen N, Mark AE, '''Nair PC''', van Gunsteren WF. Comparison of Enveloping Distribution Sampling and Thermodynamic Integration to Calculate Binding Free Energies of Phenylethanolamine N-Methyltransferase Inhibitors. ''J Chem Phys.'' 2011 Jul;135(2):024105-13 <br> [http://dx.doi.org/10.1063/1.3604534 DOI:10.1063/1.3604534]<br />
<br />
3.'''Nair PC''', Malde AK, Mark AE."Using theory to reconcile experiment: the structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-MethylTransferase (PNMT)". ''J Chem Theory Comput.'' 2011, May;7(5):1458-1468 <br> [http://dx.doi.org/10.1021/ct1007229 DOI: 10.1021/ct1007229]<br />
<br />
4.'''Nair PC'''. "Molecular Field Analysis (MFA) and other QSAR techniques in development of phosphatase inhibitors".<br />
''Anticancer Agents Med Chem.'' 2011 Jan;11(1):151-163. (Invited Review Article) <br> [http://dx.doi.org/10.2174/187152011794941181 DOI: 10.2174/187152011794941181]<br />
<br />
5.'''Nair PC''', Sobhia ME. "Fingerprint directed scaffold hopping for identification of CCR2 antagonists".<br />
''J Chem Inf Model.'' 2008 Sep;48(9):1891-902. <br> [http://dx.doi.org/10.1021/ci800157j DOI: 10.1021/ci800157j]<br />
<br />
6.'''Nair PC''', Srikanth K, Sobhia ME. "QSAR studies on CCR2 antagonists with chiral sensitive hologram descriptors".<br />
''Bioorg Med Chem Lett.'' 2008 Feb;18(4):1323-30. <br> doi:10.1016/j.bmcl.2008.01.023<br />
<br />
7.Srikanth K, '''Nair PC''', Sobhia ME. "Probing the structural and topological requirements for CCR2 antagonism: holographic QSAR for <br> indolopiperidine derivatives".''Bioorg Med Chem Lett.'' 2008 Feb;18(4):1450-6. <br><br />
<br />
8.'''Nair PC''', Sobhia ME. "Comparative QSTR studies for predicting mutagenicity of nitro compounds".<br />
''J Mol Graph Model.'' 2008 Feb;26(6):916-34. <br><br />
<br />
9.'''Nair PC''', Sobhia ME. "Quantitative structure activity relationship studies on thiourea analogues as influenza virus neuraminidase inhibitors". ''Eur J Med Chem.'' 2008 Feb;43(2):293-9. <br><br />
<br />
10.'''Nair PC''', Sobhia ME."CoMFA based de novo design of pyridazine analogs as PTP1B inhibitors".<br />
''J Mol Graph Model.'' 2007 Jul;26(1):117-23. <br><br />
<br />
11.Khurana J, '''Nair P''',Sobhia ME. "Design of Allosteric Ligands Using Computer Aided Drug Design (CADD) Techniques", Current Research & Information on Pharmaceutical Sciences (CRIPS), 2006 Apr;7(2):8-13.(Review Article)<br><br />
<br />
== Poster Presentations ==<br />
1.'''Nair PC''', Malde AK, Mark AE."Validation of fragment hits in X-ray crystal complexes", The East Coast Protein Meeting, Coffs Harbour NSW, Australia, 15-17th July 2011<br />
<br />
2.'''Nair PC''', Malde AK, Mark AE."The structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-methyltransferase (PNMT): A Molecular Dynamics and Free Energy study", Molecular Modelling 2010, Melbourne, Australia, 28Nov-1Dec 2010.<br />
<br />
3.'''Nair PC''', Malde AK, Mark AE.Investigating structural requirements for PNMT inhibition: A molecular dynamics and free energy calculation study", Division of chemistry and structural biology symposium, Institute of Molecular Bioscience, Brisbane, Australia, Nov 18-19 2010.<br />
<br />
4.'''Nair PC''', Malde AK, Mark AE. "Investigation of ligand interaction and binding free Energy of 1,2,3,4 tetrahydroisoquinoline analogues as PNMT inhibitors", 61st Indian Pharmaceutical Congress, 11-13 December 2009.<br />
<br />
5.'''Nair PC''', Sobhia ME. "Identification of Novel CCR2 Scaffolds Through Fingerprint Directed Virtual Screening", Virtual Discovery Europe (Computer Aided Drug Design and Screening) London, England, 24-25 October 2007. (Presented by Dr. M. Elizabeth Sobhia, NIPER )<br />
<br />
6.'''Nair PC''', Sobhia ME. "Synergistic application of target structure based alignment and 3D-QSAR study of protein tyrosine phosphatases 1B (PTP1B) inhibitors", Workshop on Pharmcoinformatics: Tools for Drug Target Identification, NIPER, India, March 14-16, 2007.<br />
<br />
7.'''Nair PC''', Sobhia ME. "Quantitative Structure Toxicity Relationship (QSTR) Studies for Predicting Mutagenicity of Nitro Compounds", International Conference on Chemoinformatics, NCL, Pune, India, Jan 22, 2007.<br />
<br />
8.'''Nair PC''', Sobhia ME. "Design of novel PTP1B inhibitors using 3D-QSAR and concept of hypothetical cavity generation", Workshop on Pharmacoinformatics: QSAR, NIPER, India, March 3-4, 2006.<br />
<br />
== Other Conferences/Scientific visits ==<br />
<br />
Structural Biology Symposium, Institute for Glycomics, Griffith University, Gold Coast, Australia, 2009. <br />
<br />
Molecular Modelling (MM2009), Gold Coast, Queensland, Australia, July 26-29 2009. <br />
<br />
Attended 8th National Center of Competence in Research (NCCR) Practical Course in the area of computational structural biology, Kandersteg, Switzerland, Jan 10-15 2010.<br />
<br />
Visited as a scientific guest in the laboratory of Prof. Wilfred F. van Gunsteren, ETH Zurich, Switzerland, Jan 16-29 2010.<br />
<br />
== Contact Details ==<br />
<br />
Endeavour IPRS Doctoral Fellow <br><br />
Molecular Dynamics Group <br><br />
School of Chemistry and Molecular Biosciences (SCMB) <br><br />
Molecular Biosciences Building (#76) <br><br />
The University of Queensland <br><br />
St. Lucia Campus, Brisbane, QLD 4072 <br><br />
Australia <br><br />
<br />
'''email''' p.nair@uq.edu.au</div>PramodNairhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Pramod_Nair&diff=15966Pramod Nair2011-08-31T03:47:52Z<p>PramodNair: /* Publications */</p>
<hr />
<div>Automated Force Field Topology Builder (ATB) for GROMOS and GROMACS : MD group of Prof. Alan E. Mark<br />
http://compbio.biosci.uq.edu.au/atb/ <br />
<br />
== Research Interests ==<br />
Computer Aided Drug Design (CADD) and Free Energy Calculations<br />
<br />
Alternate Free energy methods to aid high-throughput virtual screening in drug discovery<br />
<br />
Molecular Dynamics simulations of macromolecular and small molecular systems<br />
<br />
== Academic ==<br />
'''B. Pharm.''' Bombay College of Pharmacy, University of Mumbai, India 2001-2005 <br><br />
'''MS (Pharm.)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2005-2007 <br><br />
'''Junior Research Fellow (JRF)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2007-2008 <br><br />
'''PhD Student''' Molecular Dynamics Group, School of Chemistry and Molecular Biosciences (SCMB),University of Queensland, Australia 2009 <br><br />
<br />
== Publications ==<br />
1. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, '''Nair PC''', Oostenbrink C, Mark AE. An Automated force field Topology Builder (ATB) and repository: version 1.0. ''J Chem Theory Comput.'' 2011, submitted.<br />
<br />
2. Riniker S, Christ CD, Hansen N, Mark AE, '''Nair PC''', van Gunsteren WF. Comparison of Enveloping Distribution Sampling and Thermodynamic Integration to Calculate Binding Free Energies of Phenylethanolamine N-Methyltransferase Inhibitors. ''J Chem Phys.'' 2011 Jul;135(2):024105-13 <br> [http://dx.doi.org/10.1063/1.3604534 DOI:10.1063/1.3604534]<br />
<br />
3.'''Nair PC''', Malde AK, Mark AE."Using theory to reconcile experiment: the structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-MethylTransferase (PNMT)". ''J Chem Theory Comput.'' 2011, May;7(5):1458-1468 <br> [http://dx.doi.org/10.1021/ct1007229 DOI: 10.1021/ct1007229]<br />
<br />
4.'''Nair PC'''. "Molecular Field Analysis (MFA) and other QSAR techniques in development of phosphatase inhibitors".<br />
''Anticancer Agents Med Chem.'' 2011 Jan;11(1):151-163. (Invited Review Article) <br> [http://dx.doi.org/10.2174/187152011794941181 DOI: 10.2174/187152011794941181]<br />
<br />
5.'''Nair PC''', Sobhia ME. "Fingerprint directed scaffold hopping for identification of CCR2 antagonists".<br />
''J Chem Inf Model.'' 2008 Sep;48(9):1891-902. <br><br />
<br />
6.'''Nair PC''', Srikanth K, Sobhia ME. "QSAR studies on CCR2 antagonists with chiral sensitive hologram descriptors".<br />
''Bioorg Med Chem Lett.'' 2008 Feb;18(4):1323-30. <br><br />
<br />
7.Srikanth K, '''Nair PC''', Sobhia ME. "Probing the structural and topological requirements for CCR2 antagonism: holographic QSAR for <br> indolopiperidine derivatives".''Bioorg Med Chem Lett.'' 2008 Feb;18(4):1450-6. <br><br />
<br />
8.'''Nair PC''', Sobhia ME. "Comparative QSTR studies for predicting mutagenicity of nitro compounds".<br />
''J Mol Graph Model.'' 2008 Feb;26(6):916-34. <br><br />
<br />
9.'''Nair PC''', Sobhia ME. "Quantitative structure activity relationship studies on thiourea analogues as influenza virus neuraminidase inhibitors". ''Eur J Med Chem.'' 2008 Feb;43(2):293-9. <br><br />
<br />
10.'''Nair PC''', Sobhia ME."CoMFA based de novo design of pyridazine analogs as PTP1B inhibitors".<br />
''J Mol Graph Model.'' 2007 Jul;26(1):117-23. <br><br />
<br />
11.Khurana J, '''Nair P''',Sobhia ME. "Design of Allosteric Ligands Using Computer Aided Drug Design (CADD) Techniques", Current Research & Information on Pharmaceutical Sciences (CRIPS), 2006 Apr;7(2):8-13.(Review Article)<br><br />
<br />
== Poster Presentations ==<br />
1.'''Nair PC''', Malde AK, Mark AE."Validation of fragment hits in X-ray crystal complexes", The East Coast Protein Meeting, Coffs Harbour NSW, Australia, 15-17th July 2011<br />
<br />
2.'''Nair PC''', Malde AK, Mark AE."The structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-methyltransferase (PNMT): A Molecular Dynamics and Free Energy study", Molecular Modelling 2010, Melbourne, Australia, 28Nov-1Dec 2010.<br />
<br />
3.'''Nair PC''', Malde AK, Mark AE.Investigating structural requirements for PNMT inhibition: A molecular dynamics and free energy calculation study", Division of chemistry and structural biology symposium, Institute of Molecular Bioscience, Brisbane, Australia, Nov 18-19 2010.<br />
<br />
4.'''Nair PC''', Malde AK, Mark AE. "Investigation of ligand interaction and binding free Energy of 1,2,3,4 tetrahydroisoquinoline analogues as PNMT inhibitors", 61st Indian Pharmaceutical Congress, 11-13 December 2009.<br />
<br />
5.'''Nair PC''', Sobhia ME. "Identification of Novel CCR2 Scaffolds Through Fingerprint Directed Virtual Screening", Virtual Discovery Europe (Computer Aided Drug Design and Screening) London, England, 24-25 October 2007. (Presented by Dr. M. Elizabeth Sobhia, NIPER )<br />
<br />
6.'''Nair PC''', Sobhia ME. "Synergistic application of target structure based alignment and 3D-QSAR study of protein tyrosine phosphatases 1B (PTP1B) inhibitors", Workshop on Pharmcoinformatics: Tools for Drug Target Identification, NIPER, India, March 14-16, 2007.<br />
<br />
7.'''Nair PC''', Sobhia ME. "Quantitative Structure Toxicity Relationship (QSTR) Studies for Predicting Mutagenicity of Nitro Compounds", International Conference on Chemoinformatics, NCL, Pune, India, Jan 22, 2007.<br />
<br />
8.'''Nair PC''', Sobhia ME. "Design of novel PTP1B inhibitors using 3D-QSAR and concept of hypothetical cavity generation", Workshop on Pharmacoinformatics: QSAR, NIPER, India, March 3-4, 2006.<br />
<br />
== Other Conferences/Scientific visits ==<br />
<br />
Structural Biology Symposium, Institute for Glycomics, Griffith University, Gold Coast, Australia, 2009. <br />
<br />
Molecular Modelling (MM2009), Gold Coast, Queensland, Australia, July 26-29 2009. <br />
<br />
Attended 8th National Center of Competence in Research (NCCR) Practical Course in the area of computational structural biology, Kandersteg, Switzerland, Jan 10-15 2010.<br />
<br />
Visited as a scientific guest in the laboratory of Prof. Wilfred F. van Gunsteren, ETH Zurich, Switzerland, Jan 16-29 2010.<br />
<br />
== Contact Details ==<br />
<br />
Endeavour IPRS Doctoral Fellow <br><br />
Molecular Dynamics Group <br><br />
School of Chemistry and Molecular Biosciences (SCMB) <br><br />
Molecular Biosciences Building (#76) <br><br />
The University of Queensland <br><br />
St. Lucia Campus, Brisbane, QLD 4072 <br><br />
Australia <br><br />
<br />
'''email''' p.nair@uq.edu.au</div>PramodNairhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Pramod_Nair&diff=15965Pramod Nair2011-08-31T03:39:45Z<p>PramodNair: /* Publications */</p>
<hr />
<div>Automated Force Field Topology Builder (ATB) for GROMOS and GROMACS : MD group of Prof. Alan E. Mark<br />
http://compbio.biosci.uq.edu.au/atb/ <br />
<br />
== Research Interests ==<br />
Computer Aided Drug Design (CADD) and Free Energy Calculations<br />
<br />
Alternate Free energy methods to aid high-throughput virtual screening in drug discovery<br />
<br />
Molecular Dynamics simulations of macromolecular and small molecular systems<br />
<br />
== Academic ==<br />
'''B. Pharm.''' Bombay College of Pharmacy, University of Mumbai, India 2001-2005 <br><br />
'''MS (Pharm.)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2005-2007 <br><br />
'''Junior Research Fellow (JRF)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2007-2008 <br><br />
'''PhD Student''' Molecular Dynamics Group, School of Chemistry and Molecular Biosciences (SCMB),University of Queensland, Australia 2009 <br><br />
<br />
== Publications ==<br />
1. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, '''Nair PC''', Oostenbrink C, Mark AE. An Automated force field Topology Builder (ATB) and repository: version 1.0. ''J Chem Theory Comput.'' 2011, submitted.<br />
<br />
2. Riniker S, Christ CD, Hansen N, Mark AE, '''Nair PC''', van Gunsteren WF. Comparison of Enveloping Distribution Sampling and Thermodynamic Integration to Calculate Binding Free Energies of Phenylethanolamine N-Methyltransferase Inhibitors. ''J Chem Phys.'' 2011 Jul;135(2):024105-13 <br> [http://dx.doi.org/10.1063/1.3604534 DOI:10.1063/1.3604534]<br />
<br />
3.'''Nair PC''', Malde AK, Mark AE."Using theory to reconcile experiment: the structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-MethylTransferase (PNMT)". ''J Chem Theory Comput.'' 2011, May;7(5):1458-1468 <br> [http://dx.doi.org/10.1021/ct1007229 DOI: 10.1021/ct1007229]<br />
<br />
4.'''Nair PC'''. "Molecular Field Analysis (MFA) and other QSAR techniques in development of phosphatase inhibitors".<br />
''Anticancer Agents Med Chem.'' 2011 Jan;11(1):151-163. (Invited Review Article) <br><br />
<br />
5.'''Nair PC''', Sobhia ME. "Fingerprint directed scaffold hopping for identification of CCR2 antagonists".<br />
''J Chem Inf Model.'' 2008 Sep;48(9):1891-902. <br><br />
<br />
6.'''Nair PC''', Srikanth K, Sobhia ME. "QSAR studies on CCR2 antagonists with chiral sensitive hologram descriptors".<br />
''Bioorg Med Chem Lett.'' 2008 Feb;18(4):1323-30. <br><br />
<br />
7.Srikanth K, '''Nair PC''', Sobhia ME. "Probing the structural and topological requirements for CCR2 antagonism: holographic QSAR for <br> indolopiperidine derivatives".''Bioorg Med Chem Lett.'' 2008 Feb;18(4):1450-6. <br><br />
<br />
8.'''Nair PC''', Sobhia ME. "Comparative QSTR studies for predicting mutagenicity of nitro compounds".<br />
''J Mol Graph Model.'' 2008 Feb;26(6):916-34. <br><br />
<br />
9.'''Nair PC''', Sobhia ME. "Quantitative structure activity relationship studies on thiourea analogues as influenza virus neuraminidase inhibitors". ''Eur J Med Chem.'' 2008 Feb;43(2):293-9. <br><br />
<br />
10.'''Nair PC''', Sobhia ME."CoMFA based de novo design of pyridazine analogs as PTP1B inhibitors".<br />
''J Mol Graph Model.'' 2007 Jul;26(1):117-23. <br><br />
<br />
11.Khurana J, '''Nair P''',Sobhia ME. "Design of Allosteric Ligands Using Computer Aided Drug Design (CADD) Techniques", Current Research & Information on Pharmaceutical Sciences (CRIPS), 2006 Apr;7(2):8-13.(Review Article)<br><br />
<br />
== Poster Presentations ==<br />
1.'''Nair PC''', Malde AK, Mark AE."Validation of fragment hits in X-ray crystal complexes", The East Coast Protein Meeting, Coffs Harbour NSW, Australia, 15-17th July 2011<br />
<br />
2.'''Nair PC''', Malde AK, Mark AE."The structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-methyltransferase (PNMT): A Molecular Dynamics and Free Energy study", Molecular Modelling 2010, Melbourne, Australia, 28Nov-1Dec 2010.<br />
<br />
3.'''Nair PC''', Malde AK, Mark AE.Investigating structural requirements for PNMT inhibition: A molecular dynamics and free energy calculation study", Division of chemistry and structural biology symposium, Institute of Molecular Bioscience, Brisbane, Australia, Nov 18-19 2010.<br />
<br />
4.'''Nair PC''', Malde AK, Mark AE. "Investigation of ligand interaction and binding free Energy of 1,2,3,4 tetrahydroisoquinoline analogues as PNMT inhibitors", 61st Indian Pharmaceutical Congress, 11-13 December 2009.<br />
<br />
5.'''Nair PC''', Sobhia ME. "Identification of Novel CCR2 Scaffolds Through Fingerprint Directed Virtual Screening", Virtual Discovery Europe (Computer Aided Drug Design and Screening) London, England, 24-25 October 2007. (Presented by Dr. M. Elizabeth Sobhia, NIPER )<br />
<br />
6.'''Nair PC''', Sobhia ME. "Synergistic application of target structure based alignment and 3D-QSAR study of protein tyrosine phosphatases 1B (PTP1B) inhibitors", Workshop on Pharmcoinformatics: Tools for Drug Target Identification, NIPER, India, March 14-16, 2007.<br />
<br />
7.'''Nair PC''', Sobhia ME. "Quantitative Structure Toxicity Relationship (QSTR) Studies for Predicting Mutagenicity of Nitro Compounds", International Conference on Chemoinformatics, NCL, Pune, India, Jan 22, 2007.<br />
<br />
8.'''Nair PC''', Sobhia ME. "Design of novel PTP1B inhibitors using 3D-QSAR and concept of hypothetical cavity generation", Workshop on Pharmacoinformatics: QSAR, NIPER, India, March 3-4, 2006.<br />
<br />
== Other Conferences/Scientific visits ==<br />
<br />
Structural Biology Symposium, Institute for Glycomics, Griffith University, Gold Coast, Australia, 2009. <br />
<br />
Molecular Modelling (MM2009), Gold Coast, Queensland, Australia, July 26-29 2009. <br />
<br />
Attended 8th National Center of Competence in Research (NCCR) Practical Course in the area of computational structural biology, Kandersteg, Switzerland, Jan 10-15 2010.<br />
<br />
Visited as a scientific guest in the laboratory of Prof. Wilfred F. van Gunsteren, ETH Zurich, Switzerland, Jan 16-29 2010.<br />
<br />
== Contact Details ==<br />
<br />
Endeavour IPRS Doctoral Fellow <br><br />
Molecular Dynamics Group <br><br />
School of Chemistry and Molecular Biosciences (SCMB) <br><br />
Molecular Biosciences Building (#76) <br><br />
The University of Queensland <br><br />
St. Lucia Campus, Brisbane, QLD 4072 <br><br />
Australia <br><br />
<br />
'''email''' p.nair@uq.edu.au</div>PramodNairhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Pramod_Nair&diff=15964Pramod Nair2011-08-31T02:44:07Z<p>PramodNair: /* Publications */</p>
<hr />
<div>Automated Force Field Topology Builder (ATB) for GROMOS and GROMACS : MD group of Prof. Alan E. Mark<br />
http://compbio.biosci.uq.edu.au/atb/ <br />
<br />
== Research Interests ==<br />
Computer Aided Drug Design (CADD) and Free Energy Calculations<br />
<br />
Alternate Free energy methods to aid high-throughput virtual screening in drug discovery<br />
<br />
Molecular Dynamics simulations of macromolecular and small molecular systems<br />
<br />
== Academic ==<br />
'''B. Pharm.''' Bombay College of Pharmacy, University of Mumbai, India 2001-2005 <br><br />
'''MS (Pharm.)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2005-2007 <br><br />
'''Junior Research Fellow (JRF)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2007-2008 <br><br />
'''PhD Student''' Molecular Dynamics Group, School of Chemistry and Molecular Biosciences (SCMB),University of Queensland, Australia 2009 <br><br />
<br />
== Publications ==<br />
1. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, '''Nair PC''', Oostenbrink C, Mark AE. An Automated force field Topology Builder (ATB) and repository: version 1.0. ''J Chem Theory Comput.'' 2011, submitted.<br />
<br />
2. Riniker S, Christ CD, Hansen N, Mark AE, '''Nair PC''', van Gunsteren WF. Comparison of Enveloping Distribution Sampling and Thermodynamic Integration to Calculate Binding Free Energies of Phenylethanolamine N-Methyltransferase Inhibitors. ''J Chem Phys.'' 2011 Jul;135(2):024105-13 <br> [http://dx.doi.org/10.1063/1.3604534 DOI:10.1063/1.3604534]<br />
<br />
3.'''Nair PC''', Malde AK, Mark AE."Using theory to reconcile experiment: the structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-MethylTransferase (PNMT)". ''J Chem Theory Comput.'' 2011, May;7(5):1458-1468 <br><br />
<br />
4.'''Nair PC'''. "Molecular Field Analysis (MFA) and other QSAR techniques in development of phosphatase inhibitors".<br />
''Anticancer Agents Med Chem.'' 2011 Jan;11(1):151-163. (Invited Review Article) <br><br />
<br />
5.'''Nair PC''', Sobhia ME. "Fingerprint directed scaffold hopping for identification of CCR2 antagonists".<br />
''J Chem Inf Model.'' 2008 Sep;48(9):1891-902. <br><br />
<br />
6.'''Nair PC''', Srikanth K, Sobhia ME. "QSAR studies on CCR2 antagonists with chiral sensitive hologram descriptors".<br />
''Bioorg Med Chem Lett.'' 2008 Feb;18(4):1323-30. <br><br />
<br />
7.Srikanth K, '''Nair PC''', Sobhia ME. "Probing the structural and topological requirements for CCR2 antagonism: holographic QSAR for <br> indolopiperidine derivatives".''Bioorg Med Chem Lett.'' 2008 Feb;18(4):1450-6. <br><br />
<br />
8.'''Nair PC''', Sobhia ME. "Comparative QSTR studies for predicting mutagenicity of nitro compounds".<br />
''J Mol Graph Model.'' 2008 Feb;26(6):916-34. <br><br />
<br />
9.'''Nair PC''', Sobhia ME. "Quantitative structure activity relationship studies on thiourea analogues as influenza virus neuraminidase inhibitors". ''Eur J Med Chem.'' 2008 Feb;43(2):293-9. <br><br />
<br />
10.'''Nair PC''', Sobhia ME."CoMFA based de novo design of pyridazine analogs as PTP1B inhibitors".<br />
''J Mol Graph Model.'' 2007 Jul;26(1):117-23. <br><br />
<br />
11.Khurana J, '''Nair P''',Sobhia ME. "Design of Allosteric Ligands Using Computer Aided Drug Design (CADD) Techniques", Current Research & Information on Pharmaceutical Sciences (CRIPS), 2006 Apr;7(2):8-13.(Review Article)<br><br />
<br />
== Poster Presentations ==<br />
1.'''Nair PC''', Malde AK, Mark AE."Validation of fragment hits in X-ray crystal complexes", The East Coast Protein Meeting, Coffs Harbour NSW, Australia, 15-17th July 2011<br />
<br />
2.'''Nair PC''', Malde AK, Mark AE."The structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-methyltransferase (PNMT): A Molecular Dynamics and Free Energy study", Molecular Modelling 2010, Melbourne, Australia, 28Nov-1Dec 2010.<br />
<br />
3.'''Nair PC''', Malde AK, Mark AE.Investigating structural requirements for PNMT inhibition: A molecular dynamics and free energy calculation study", Division of chemistry and structural biology symposium, Institute of Molecular Bioscience, Brisbane, Australia, Nov 18-19 2010.<br />
<br />
4.'''Nair PC''', Malde AK, Mark AE. "Investigation of ligand interaction and binding free Energy of 1,2,3,4 tetrahydroisoquinoline analogues as PNMT inhibitors", 61st Indian Pharmaceutical Congress, 11-13 December 2009.<br />
<br />
5.'''Nair PC''', Sobhia ME. "Identification of Novel CCR2 Scaffolds Through Fingerprint Directed Virtual Screening", Virtual Discovery Europe (Computer Aided Drug Design and Screening) London, England, 24-25 October 2007. (Presented by Dr. M. Elizabeth Sobhia, NIPER )<br />
<br />
6.'''Nair PC''', Sobhia ME. "Synergistic application of target structure based alignment and 3D-QSAR study of protein tyrosine phosphatases 1B (PTP1B) inhibitors", Workshop on Pharmcoinformatics: Tools for Drug Target Identification, NIPER, India, March 14-16, 2007.<br />
<br />
7.'''Nair PC''', Sobhia ME. "Quantitative Structure Toxicity Relationship (QSTR) Studies for Predicting Mutagenicity of Nitro Compounds", International Conference on Chemoinformatics, NCL, Pune, India, Jan 22, 2007.<br />
<br />
8.'''Nair PC''', Sobhia ME. "Design of novel PTP1B inhibitors using 3D-QSAR and concept of hypothetical cavity generation", Workshop on Pharmacoinformatics: QSAR, NIPER, India, March 3-4, 2006.<br />
<br />
== Other Conferences/Scientific visits ==<br />
<br />
Structural Biology Symposium, Institute for Glycomics, Griffith University, Gold Coast, Australia, 2009. <br />
<br />
Molecular Modelling (MM2009), Gold Coast, Queensland, Australia, July 26-29 2009. <br />
<br />
Attended 8th National Center of Competence in Research (NCCR) Practical Course in the area of computational structural biology, Kandersteg, Switzerland, Jan 10-15 2010.<br />
<br />
Visited as a scientific guest in the laboratory of Prof. Wilfred F. van Gunsteren, ETH Zurich, Switzerland, Jan 16-29 2010.<br />
<br />
== Contact Details ==<br />
<br />
Endeavour IPRS Doctoral Fellow <br><br />
Molecular Dynamics Group <br><br />
School of Chemistry and Molecular Biosciences (SCMB) <br><br />
Molecular Biosciences Building (#76) <br><br />
The University of Queensland <br><br />
St. Lucia Campus, Brisbane, QLD 4072 <br><br />
Australia <br><br />
<br />
'''email''' p.nair@uq.edu.au</div>PramodNairhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Pramod_Nair&diff=15956Pramod Nair2011-07-21T05:51:47Z<p>PramodNair: /* Poster Presentations */</p>
<hr />
<div>Automated Force Field Topology Builder (ATB) for GROMOS and GROMACS : MD group of Prof. Alan E. Mark<br />
http://compbio.biosci.uq.edu.au/atb/ <br />
<br />
== Research Interests ==<br />
Computer Aided Drug Design (CADD) and Free Energy Calculations<br />
<br />
Alternate Free energy methods to aid high-throughput virtual screening in drug discovery<br />
<br />
Molecular Dynamics simulations of macromolecular and small molecular systems<br />
<br />
== Academic ==<br />
'''B. Pharm.''' Bombay College of Pharmacy, University of Mumbai, India 2001-2005 <br><br />
'''MS (Pharm.)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2005-2007 <br><br />
'''Junior Research Fellow (JRF)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2007-2008 <br><br />
'''PhD Student''' Molecular Dynamics Group, School of Chemistry and Molecular Biosciences (SCMB),University of Queensland, Australia 2009 <br><br />
<br />
== Publications ==<br />
1. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, '''Nair PC''', Oostenbrink C, Mark AE. An Automated force field Topology Builder (ATB) and repository: version 1.0. ''J Chem Theory Comput.'' 2011, submitted.<br />
<br />
2. Riniker S, Christ CD, Hansen N, Mark AE, '''Nair PC''', van Gunsteren WF. Comparison of Enveloping Distribution Sampling and Thermodynamic Integration to Calculate Binding Free Energies of Phenylethanolamine N-Methyltransferase Inhibitors. ''J Chem Phys.'' 2011 Jul;135(2):024105-13 <br> <br />
<br />
3.'''Nair PC''', Malde AK, Mark AE."Using theory to reconcile experiment: the structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-MethylTransferase (PNMT)". ''J Chem Theory Comput.'' 2011, May;7(5):1458-1468 <br><br />
<br />
4.'''Nair PC'''. "Molecular Field Analysis (MFA) and other QSAR techniques in development of phosphatase inhibitors".<br />
''Anticancer Agents Med Chem.'' 2011 Jan;11(1):151-163. (Invited Review Article) <br><br />
<br />
5.'''Nair PC''', Sobhia ME. "Fingerprint directed scaffold hopping for identification of CCR2 antagonists".<br />
''J Chem Inf Model.'' 2008 Sep;48(9):1891-902. <br><br />
<br />
6.'''Nair PC''', Srikanth K, Sobhia ME. "QSAR studies on CCR2 antagonists with chiral sensitive hologram descriptors".<br />
''Bioorg Med Chem Lett.'' 2008 Feb;18(4):1323-30. <br><br />
<br />
7.Srikanth K, '''Nair PC''', Sobhia ME. "Probing the structural and topological requirements for CCR2 antagonism: holographic QSAR for <br> indolopiperidine derivatives".''Bioorg Med Chem Lett.'' 2008 Feb;18(4):1450-6. <br><br />
<br />
8.'''Nair PC''', Sobhia ME. "Comparative QSTR studies for predicting mutagenicity of nitro compounds".<br />
''J Mol Graph Model.'' 2008 Feb;26(6):916-34. <br><br />
<br />
9.'''Nair PC''', Sobhia ME. "Quantitative structure activity relationship studies on thiourea analogues as influenza virus neuraminidase inhibitors". ''Eur J Med Chem.'' 2008 Feb;43(2):293-9. <br><br />
<br />
10.'''Nair PC''', Sobhia ME."CoMFA based de novo design of pyridazine analogs as PTP1B inhibitors".<br />
''J Mol Graph Model.'' 2007 Jul;26(1):117-23. <br><br />
<br />
11.Khurana J, '''Nair P''',Sobhia ME. "Design of Allosteric Ligands Using Computer Aided Drug Design (CADD) Techniques", Current Research & Information on Pharmaceutical Sciences (CRIPS), 2006 Apr;7(2):8-13.(Review Article)<br><br />
<br />
== Poster Presentations ==<br />
1.'''Nair PC''', Malde AK, Mark AE."Validation of fragment hits in X-ray crystal complexes", The East Coast Protein Meeting, Coffs Harbour NSW, Australia, 15-17th July 2011<br />
<br />
2.'''Nair PC''', Malde AK, Mark AE."The structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-methyltransferase (PNMT): A Molecular Dynamics and Free Energy study", Molecular Modelling 2010, Melbourne, Australia, 28Nov-1Dec 2010.<br />
<br />
3.'''Nair PC''', Malde AK, Mark AE.Investigating structural requirements for PNMT inhibition: A molecular dynamics and free energy calculation study", Division of chemistry and structural biology symposium, Institute of Molecular Bioscience, Brisbane, Australia, Nov 18-19 2010.<br />
<br />
4.'''Nair PC''', Malde AK, Mark AE. "Investigation of ligand interaction and binding free Energy of 1,2,3,4 tetrahydroisoquinoline analogues as PNMT inhibitors", 61st Indian Pharmaceutical Congress, 11-13 December 2009.<br />
<br />
5.'''Nair PC''', Sobhia ME. "Identification of Novel CCR2 Scaffolds Through Fingerprint Directed Virtual Screening", Virtual Discovery Europe (Computer Aided Drug Design and Screening) London, England, 24-25 October 2007. (Presented by Dr. M. Elizabeth Sobhia, NIPER )<br />
<br />
6.'''Nair PC''', Sobhia ME. "Synergistic application of target structure based alignment and 3D-QSAR study of protein tyrosine phosphatases 1B (PTP1B) inhibitors", Workshop on Pharmcoinformatics: Tools for Drug Target Identification, NIPER, India, March 14-16, 2007.<br />
<br />
7.'''Nair PC''', Sobhia ME. "Quantitative Structure Toxicity Relationship (QSTR) Studies for Predicting Mutagenicity of Nitro Compounds", International Conference on Chemoinformatics, NCL, Pune, India, Jan 22, 2007.<br />
<br />
8.'''Nair PC''', Sobhia ME. "Design of novel PTP1B inhibitors using 3D-QSAR and concept of hypothetical cavity generation", Workshop on Pharmacoinformatics: QSAR, NIPER, India, March 3-4, 2006.<br />
<br />
== Other Conferences/Scientific visits ==<br />
<br />
Structural Biology Symposium, Institute for Glycomics, Griffith University, Gold Coast, Australia, 2009. <br />
<br />
Molecular Modelling (MM2009), Gold Coast, Queensland, Australia, July 26-29 2009. <br />
<br />
Attended 8th National Center of Competence in Research (NCCR) Practical Course in the area of computational structural biology, Kandersteg, Switzerland, Jan 10-15 2010.<br />
<br />
Visited as a scientific guest in the laboratory of Prof. Wilfred F. van Gunsteren, ETH Zurich, Switzerland, Jan 16-29 2010.<br />
<br />
== Contact Details ==<br />
<br />
Endeavour IPRS Doctoral Fellow <br><br />
Molecular Dynamics Group <br><br />
School of Chemistry and Molecular Biosciences (SCMB) <br><br />
Molecular Biosciences Building (#76) <br><br />
The University of Queensland <br><br />
St. Lucia Campus, Brisbane, QLD 4072 <br><br />
Australia <br><br />
<br />
'''email''' p.nair@uq.edu.au</div>PramodNairhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Pramod_Nair&diff=15955Pramod Nair2011-07-18T01:17:38Z<p>PramodNair: /* Other Conferences/Scientific visits */</p>
<hr />
<div>Automated Force Field Topology Builder (ATB) for GROMOS and GROMACS : MD group of Prof. Alan E. Mark<br />
http://compbio.biosci.uq.edu.au/atb/ <br />
<br />
== Research Interests ==<br />
Computer Aided Drug Design (CADD) and Free Energy Calculations<br />
<br />
Alternate Free energy methods to aid high-throughput virtual screening in drug discovery<br />
<br />
Molecular Dynamics simulations of macromolecular and small molecular systems<br />
<br />
== Academic ==<br />
'''B. Pharm.''' Bombay College of Pharmacy, University of Mumbai, India 2001-2005 <br><br />
'''MS (Pharm.)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2005-2007 <br><br />
'''Junior Research Fellow (JRF)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2007-2008 <br><br />
'''PhD Student''' Molecular Dynamics Group, School of Chemistry and Molecular Biosciences (SCMB),University of Queensland, Australia 2009 <br><br />
<br />
== Publications ==<br />
1. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, '''Nair PC''', Oostenbrink C, Mark AE. An Automated force field Topology Builder (ATB) and repository: version 1.0. ''J Chem Theory Comput.'' 2011, submitted.<br />
<br />
2. Riniker S, Christ CD, Hansen N, Mark AE, '''Nair PC''', van Gunsteren WF. Comparison of Enveloping Distribution Sampling and Thermodynamic Integration to Calculate Binding Free Energies of Phenylethanolamine N-Methyltransferase Inhibitors. ''J Chem Phys.'' 2011 Jul;135(2):024105-13 <br> <br />
<br />
3.'''Nair PC''', Malde AK, Mark AE."Using theory to reconcile experiment: the structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-MethylTransferase (PNMT)". ''J Chem Theory Comput.'' 2011, May;7(5):1458-1468 <br><br />
<br />
4.'''Nair PC'''. "Molecular Field Analysis (MFA) and other QSAR techniques in development of phosphatase inhibitors".<br />
''Anticancer Agents Med Chem.'' 2011 Jan;11(1):151-163. (Invited Review Article) <br><br />
<br />
5.'''Nair PC''', Sobhia ME. "Fingerprint directed scaffold hopping for identification of CCR2 antagonists".<br />
''J Chem Inf Model.'' 2008 Sep;48(9):1891-902. <br><br />
<br />
6.'''Nair PC''', Srikanth K, Sobhia ME. "QSAR studies on CCR2 antagonists with chiral sensitive hologram descriptors".<br />
''Bioorg Med Chem Lett.'' 2008 Feb;18(4):1323-30. <br><br />
<br />
7.Srikanth K, '''Nair PC''', Sobhia ME. "Probing the structural and topological requirements for CCR2 antagonism: holographic QSAR for <br> indolopiperidine derivatives".''Bioorg Med Chem Lett.'' 2008 Feb;18(4):1450-6. <br><br />
<br />
8.'''Nair PC''', Sobhia ME. "Comparative QSTR studies for predicting mutagenicity of nitro compounds".<br />
''J Mol Graph Model.'' 2008 Feb;26(6):916-34. <br><br />
<br />
9.'''Nair PC''', Sobhia ME. "Quantitative structure activity relationship studies on thiourea analogues as influenza virus neuraminidase inhibitors". ''Eur J Med Chem.'' 2008 Feb;43(2):293-9. <br><br />
<br />
10.'''Nair PC''', Sobhia ME."CoMFA based de novo design of pyridazine analogs as PTP1B inhibitors".<br />
''J Mol Graph Model.'' 2007 Jul;26(1):117-23. <br><br />
<br />
11.Khurana J, '''Nair P''',Sobhia ME. "Design of Allosteric Ligands Using Computer Aided Drug Design (CADD) Techniques", Current Research & Information on Pharmaceutical Sciences (CRIPS), 2006 Apr;7(2):8-13.(Review Article)<br><br />
<br />
== Poster Presentations ==<br />
1.'''Nair PC''', Malde AK, Mark AE."Validation of fragment hits in X-ray crystal complexes", The East Coast Protein Meeting, Coffs Harbour NSW, Australia, To be presented on 15-17th July 2011<br />
<br />
2.'''Nair PC''', Malde AK, Mark AE."The structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-methyltransferase (PNMT): A Molecular Dynamics and Free Energy study", Molecular Modelling 2010, Melbourne, Australia, 28Nov-1Dec 2010.<br />
<br />
3.'''Nair PC''', Malde AK, Mark AE.Investigating structural requirements for PNMT inhibition: A molecular dynamics and free energy calculation study", Division of chemistry and structural biology symposium, Institute of Molecular Bioscience, Brisbane, Australia, Nov 18-19 2010.<br />
<br />
4.'''Nair PC''', Malde AK, Mark AE. "Investigation of ligand interaction and binding free Energy of 1,2,3,4 tetrahydroisoquinoline analogues as PNMT inhibitors", 61st Indian Pharmaceutical Congress, 11-13 December 2009.<br />
<br />
5.'''Nair PC''', Sobhia ME. "Identification of Novel CCR2 Scaffolds Through Fingerprint Directed Virtual Screening", Virtual Discovery Europe (Computer Aided Drug Design and Screening) London, England, 24-25 October 2007. (Presented by Dr. M. Elizabeth Sobhia, NIPER )<br />
<br />
6.'''Nair PC''', Sobhia ME. "Synergistic application of target structure based alignment and 3D-QSAR study of protein tyrosine phosphatases 1B (PTP1B) inhibitors", Workshop on Pharmcoinformatics: Tools for Drug Target Identification, NIPER, India, March 14-16, 2007.<br />
<br />
7.'''Nair PC''', Sobhia ME. "Quantitative Structure Toxicity Relationship (QSTR) Studies for Predicting Mutagenicity of Nitro Compounds", International Conference on Chemoinformatics, NCL, Pune, India, Jan 22, 2007.<br />
<br />
8.'''Nair PC''', Sobhia ME. "Design of novel PTP1B inhibitors using 3D-QSAR and concept of hypothetical cavity generation", Workshop on Pharmacoinformatics: QSAR, NIPER, India, March 3-4, 2006.<br />
<br />
== Other Conferences/Scientific visits ==<br />
<br />
Structural Biology Symposium, Institute for Glycomics, Griffith University, Gold Coast, Australia, 2009. <br />
<br />
Molecular Modelling (MM2009), Gold Coast, Queensland, Australia, July 26-29 2009. <br />
<br />
Attended 8th National Center of Competence in Research (NCCR) Practical Course in the area of computational structural biology, Kandersteg, Switzerland, Jan 10-15 2010.<br />
<br />
Visited as a scientific guest in the laboratory of Prof. Wilfred F. van Gunsteren, ETH Zurich, Switzerland, Jan 16-29 2010.<br />
<br />
== Contact Details ==<br />
<br />
Endeavour IPRS Doctoral Fellow <br><br />
Molecular Dynamics Group <br><br />
School of Chemistry and Molecular Biosciences (SCMB) <br><br />
Molecular Biosciences Building (#76) <br><br />
The University of Queensland <br><br />
St. Lucia Campus, Brisbane, QLD 4072 <br><br />
Australia <br><br />
<br />
'''email''' p.nair@uq.edu.au</div>PramodNairhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Pramod_Nair&diff=15951Pramod Nair2011-07-12T02:10:19Z<p>PramodNair: /* Publications */</p>
<hr />
<div>Automated Force Field Topology Builder (ATB) for GROMOS and GROMACS : MD group of Prof. Alan E. Mark<br />
http://compbio.biosci.uq.edu.au/atb/ <br />
<br />
== Research Interests ==<br />
Computer Aided Drug Design (CADD) and Free Energy Calculations<br />
<br />
Alternate Free energy methods to aid high-throughput virtual screening in drug discovery<br />
<br />
Molecular Dynamics simulations of macromolecular and small molecular systems<br />
<br />
== Academic ==<br />
'''B. Pharm.''' Bombay College of Pharmacy, University of Mumbai, India 2001-2005 <br><br />
'''MS (Pharm.)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2005-2007 <br><br />
'''Junior Research Fellow (JRF)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2007-2008 <br><br />
'''PhD Student''' Molecular Dynamics Group, School of Chemistry and Molecular Biosciences (SCMB),University of Queensland, Australia 2009 <br><br />
<br />
== Publications ==<br />
1. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, '''Nair PC''', Oostenbrink C, Mark AE. An Automated force field Topology Builder (ATB) and repository: version 1.0. ''J Chem Theory Comput.'' 2011, submitted.<br />
<br />
2. Riniker S, Christ CD, Hansen N, Mark AE, '''Nair PC''', van Gunsteren WF. Comparison of Enveloping Distribution Sampling and Thermodynamic Integration to Calculate Binding Free Energies of Phenylethanolamine N-Methyltransferase Inhibitors. ''J Chem Phys.'' 2011 Jul;135(2):024105-13 <br> <br />
<br />
3.'''Nair PC''', Malde AK, Mark AE."Using theory to reconcile experiment: the structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-MethylTransferase (PNMT)". ''J Chem Theory Comput.'' 2011, May;7(5):1458-1468 <br><br />
<br />
4.'''Nair PC'''. "Molecular Field Analysis (MFA) and other QSAR techniques in development of phosphatase inhibitors".<br />
''Anticancer Agents Med Chem.'' 2011 Jan;11(1):151-163. (Invited Review Article) <br><br />
<br />
5.'''Nair PC''', Sobhia ME. "Fingerprint directed scaffold hopping for identification of CCR2 antagonists".<br />
''J Chem Inf Model.'' 2008 Sep;48(9):1891-902. <br><br />
<br />
6.'''Nair PC''', Srikanth K, Sobhia ME. "QSAR studies on CCR2 antagonists with chiral sensitive hologram descriptors".<br />
''Bioorg Med Chem Lett.'' 2008 Feb;18(4):1323-30. <br><br />
<br />
7.Srikanth K, '''Nair PC''', Sobhia ME. "Probing the structural and topological requirements for CCR2 antagonism: holographic QSAR for <br> indolopiperidine derivatives".''Bioorg Med Chem Lett.'' 2008 Feb;18(4):1450-6. <br><br />
<br />
8.'''Nair PC''', Sobhia ME. "Comparative QSTR studies for predicting mutagenicity of nitro compounds".<br />
''J Mol Graph Model.'' 2008 Feb;26(6):916-34. <br><br />
<br />
9.'''Nair PC''', Sobhia ME. "Quantitative structure activity relationship studies on thiourea analogues as influenza virus neuraminidase inhibitors". ''Eur J Med Chem.'' 2008 Feb;43(2):293-9. <br><br />
<br />
10.'''Nair PC''', Sobhia ME."CoMFA based de novo design of pyridazine analogs as PTP1B inhibitors".<br />
''J Mol Graph Model.'' 2007 Jul;26(1):117-23. <br><br />
<br />
11.Khurana J, '''Nair P''',Sobhia ME. "Design of Allosteric Ligands Using Computer Aided Drug Design (CADD) Techniques", Current Research & Information on Pharmaceutical Sciences (CRIPS), 2006 Apr;7(2):8-13.(Review Article)<br><br />
<br />
== Poster Presentations ==<br />
1.'''Nair PC''', Malde AK, Mark AE."Validation of fragment hits in X-ray crystal complexes", The East Coast Protein Meeting, Coffs Harbour NSW, Australia, To be presented on 15-17th July 2011<br />
<br />
2.'''Nair PC''', Malde AK, Mark AE."The structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-methyltransferase (PNMT): A Molecular Dynamics and Free Energy study", Molecular Modelling 2010, Melbourne, Australia, 28Nov-1Dec 2010.<br />
<br />
3.'''Nair PC''', Malde AK, Mark AE.Investigating structural requirements for PNMT inhibition: A molecular dynamics and free energy calculation study", Division of chemistry and structural biology symposium, Institute of Molecular Bioscience, Brisbane, Australia, Nov 18-19 2010.<br />
<br />
4.'''Nair PC''', Malde AK, Mark AE. "Investigation of ligand interaction and binding free Energy of 1,2,3,4 tetrahydroisoquinoline analogues as PNMT inhibitors", 61st Indian Pharmaceutical Congress, 11-13 December 2009.<br />
<br />
5.'''Nair PC''', Sobhia ME. "Identification of Novel CCR2 Scaffolds Through Fingerprint Directed Virtual Screening", Virtual Discovery Europe (Computer Aided Drug Design and Screening) London, England, 24-25 October 2007. (Presented by Dr. M. Elizabeth Sobhia, NIPER )<br />
<br />
6.'''Nair PC''', Sobhia ME. "Synergistic application of target structure based alignment and 3D-QSAR study of protein tyrosine phosphatases 1B (PTP1B) inhibitors", Workshop on Pharmcoinformatics: Tools for Drug Target Identification, NIPER, India, March 14-16, 2007.<br />
<br />
7.'''Nair PC''', Sobhia ME. "Quantitative Structure Toxicity Relationship (QSTR) Studies for Predicting Mutagenicity of Nitro Compounds", International Conference on Chemoinformatics, NCL, Pune, India, Jan 22, 2007.<br />
<br />
8.'''Nair PC''', Sobhia ME. "Design of novel PTP1B inhibitors using 3D-QSAR and concept of hypothetical cavity generation", Workshop on Pharmacoinformatics: QSAR, NIPER, India, March 3-4, 2006.<br />
<br />
== Other Conferences/Scientific visits ==<br />
<br />
Molecular Modelling (MM2009), Gold Coast, Queensland, Australia, July 26-29 2009. <br />
<br />
Attended 8th National Center of Competence in Research (NCCR) Practical Course in the area of computational structural biology, Kandersteg, Switzerland, Jan 10-15 2010.<br />
<br />
Visited as a scientific guest in the laboratory of Prof. Wilfred F. van Gunsteren, ETH Zurich, Switzerland, Jan 16-29 2010.<br />
<br />
== Contact Details ==<br />
<br />
Endeavour IPRS Doctoral Fellow <br><br />
Molecular Dynamics Group <br><br />
School of Chemistry and Molecular Biosciences (SCMB) <br><br />
Molecular Biosciences Building (#76) <br><br />
The University of Queensland <br><br />
St. Lucia Campus, Brisbane, QLD 4072 <br><br />
Australia <br><br />
<br />
'''email''' p.nair@uq.edu.au</div>PramodNairhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Pramod_Nair&diff=15939Pramod Nair2011-06-15T12:57:21Z<p>PramodNair: /* Poster Presentations */</p>
<hr />
<div>Automated Force Field Topology Builder (ATB) for GROMOS and GROMACS : MD group of Prof. Alan E. Mark<br />
http://compbio.biosci.uq.edu.au/atb/ <br />
<br />
== Research Interests ==<br />
Computer Aided Drug Design (CADD) and Free Energy Calculations<br />
<br />
Alternate Free energy methods to aid high-throughput virtual screening in drug discovery<br />
<br />
Molecular Dynamics simulations of macromolecular and small molecular systems<br />
<br />
== Academic ==<br />
'''B. Pharm.''' Bombay College of Pharmacy, University of Mumbai, India 2001-2005 <br><br />
'''MS (Pharm.)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2005-2007 <br><br />
'''Junior Research Fellow (JRF)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2007-2008 <br><br />
'''PhD Student''' Molecular Dynamics Group, School of Chemistry and Molecular Biosciences (SCMB),University of Queensland, Australia 2009 <br><br />
<br />
== Publications ==<br />
1. Riniker S, Christ CD, Hansen N, Mark AE, '''Nair PC''', van Gunsteren WF. Comparison of Enveloping Distribution Sampling and Thermodynamic Integration to Calculate Binding Free Energies of Phenylethanolamine N-Methyltransferase Inhibitors. ''J Chem Phys.'' 2011, submitted.<br />
<br />
2. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, '''Nair PC''', Oostenbrink C, Mark AE. An Automated force field Topology Builder (ATB) and repository: version 1.0. ''J Chem Theory Comput.'' 2011, submitted.<br />
<br />
3.'''Nair PC''', Malde AK, Mark AE."Using theory to reconcile experiment: the structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-MethylTransferase (PNMT)". ''J Chem Theory Comput.'' 2011, May;7(5):1458-1468 <br><br />
<br />
4.'''Nair PC'''. "Molecular Field Analysis (MFA) and other QSAR techniques in development of phosphatase inhibitors".<br />
''Anticancer Agents Med Chem.'' 2011 Jan;11(1):151-163. (Invited Review Article) <br><br />
<br />
5.'''Nair PC''', Sobhia ME. "Fingerprint directed scaffold hopping for identification of CCR2 antagonists".<br />
''J Chem Inf Model.'' 2008 Sep;48(9):1891-902. <br><br />
<br />
6.'''Nair PC''', Srikanth K, Sobhia ME. "QSAR studies on CCR2 antagonists with chiral sensitive hologram descriptors".<br />
''Bioorg Med Chem Lett.'' 2008 Feb 15;18(4):1323-30. <br><br />
<br />
7.Srikanth K, '''Nair PC''', Sobhia ME. "Probing the structural and topological requirements for CCR2 antagonism: holographic QSAR for <br> indolopiperidine derivatives".''Bioorg Med Chem Lett.'' 2008 Feb 15;18(4):1450-6. <br><br />
<br />
8.'''Nair PC''', Sobhia ME. "Comparative QSTR studies for predicting mutagenicity of nitro compounds".<br />
''J Mol Graph Model.'' 2008 Feb;26(6):916-34. <br><br />
<br />
9.'''Nair PC''', Sobhia ME. "Quantitative structure activity relationship studies on thiourea analogues as influenza virus neuraminidase inhibitors". ''Eur J Med Chem.'' 2008 Feb;43(2):293-9. <br><br />
<br />
10.'''Nair PC''', Sobhia ME."CoMFA based de novo design of pyridazine analogs as PTP1B inhibitors".<br />
''J Mol Graph Model.'' 2007 Jul;26(1):117-23. <br><br />
<br />
11.Khurana J, '''Nair P''',Sobhia ME. "Design of Allosteric Ligands Using Computer Aided Drug Design (CADD) Techniques", Current Research & Information on Pharmaceutical Sciences (CRIPS), 2006 Apr;7(2):8-13.(Review Article)<br><br />
<br />
== Poster Presentations ==<br />
1.'''Nair PC''', Malde AK, Mark AE."Validation of fragment hits in X-ray crystal complexes", The East Coast Protein Meeting, Coffs Harbour NSW, Australia, To be presented on 15-17th July 2011<br />
<br />
2.'''Nair PC''', Malde AK, Mark AE."The structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-methyltransferase (PNMT): A Molecular Dynamics and Free Energy study", Molecular Modelling 2010, Melbourne, Australia, 28Nov-1Dec 2010.<br />
<br />
3.'''Nair PC''', Malde AK, Mark AE.Investigating structural requirements for PNMT inhibition: A molecular dynamics and free energy calculation study", Division of chemistry and structural biology symposium, Institute of Molecular Bioscience, Brisbane, Australia, Nov 18-19 2010.<br />
<br />
4.'''Nair PC''', Malde AK, Mark AE. "Investigation of ligand interaction and binding free Energy of 1,2,3,4 tetrahydroisoquinoline analogues as PNMT inhibitors", 61st Indian Pharmaceutical Congress, 11-13 December 2009.<br />
<br />
5.'''Nair PC''', Sobhia ME. "Identification of Novel CCR2 Scaffolds Through Fingerprint Directed Virtual Screening", Virtual Discovery Europe (Computer Aided Drug Design and Screening) London, England, 24-25 October 2007. (Presented by Dr. M. Elizabeth Sobhia, NIPER )<br />
<br />
6.'''Nair PC''', Sobhia ME. "Synergistic application of target structure based alignment and 3D-QSAR study of protein tyrosine phosphatases 1B (PTP1B) inhibitors", Workshop on Pharmcoinformatics: Tools for Drug Target Identification, NIPER, India, March 14-16, 2007.<br />
<br />
7.'''Nair PC''', Sobhia ME. "Quantitative Structure Toxicity Relationship (QSTR) Studies for Predicting Mutagenicity of Nitro Compounds", International Conference on Chemoinformatics, NCL, Pune, India, Jan 22, 2007.<br />
<br />
8.'''Nair PC''', Sobhia ME. "Design of novel PTP1B inhibitors using 3D-QSAR and concept of hypothetical cavity generation", Workshop on Pharmacoinformatics: QSAR, NIPER, India, March 3-4, 2006.<br />
<br />
== Other Conferences/Scientific visits ==<br />
<br />
Molecular Modelling (MM2009), Gold Coast, Queensland, Australia, July 26-29 2009. <br />
<br />
Attended 8th National Center of Competence in Research (NCCR) Practical Course in the area of computational structural biology, Kandersteg, Switzerland, Jan 10-15 2010.<br />
<br />
Visited as a scientific guest in the laboratory of Prof. Wilfred F. van Gunsteren, ETH Zurich, Switzerland, Jan 16-29 2010.<br />
<br />
== Contact Details ==<br />
<br />
Endeavour IPRS Doctoral Fellow <br><br />
Molecular Dynamics Group <br><br />
School of Chemistry and Molecular Biosciences (SCMB) <br><br />
Molecular Biosciences Building (#76) <br><br />
The University of Queensland <br><br />
St. Lucia Campus, Brisbane, QLD 4072 <br><br />
Australia <br><br />
<br />
'''email''' p.nair@uq.edu.au</div>PramodNairhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Pramod_Nair&diff=15938Pramod Nair2011-06-15T06:30:50Z<p>PramodNair: /* Poster Presentations */</p>
<hr />
<div>Automated Force Field Topology Builder (ATB) for GROMOS and GROMACS : MD group of Prof. Alan E. Mark<br />
http://compbio.biosci.uq.edu.au/atb/ <br />
<br />
== Research Interests ==<br />
Computer Aided Drug Design (CADD) and Free Energy Calculations<br />
<br />
Alternate Free energy methods to aid high-throughput virtual screening in drug discovery<br />
<br />
Molecular Dynamics simulations of macromolecular and small molecular systems<br />
<br />
== Academic ==<br />
'''B. Pharm.''' Bombay College of Pharmacy, University of Mumbai, India 2001-2005 <br><br />
'''MS (Pharm.)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2005-2007 <br><br />
'''Junior Research Fellow (JRF)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2007-2008 <br><br />
'''PhD Student''' Molecular Dynamics Group, School of Chemistry and Molecular Biosciences (SCMB),University of Queensland, Australia 2009 <br><br />
<br />
== Publications ==<br />
1. Riniker S, Christ CD, Hansen N, Mark AE, '''Nair PC''', van Gunsteren WF. Comparison of Enveloping Distribution Sampling and Thermodynamic Integration to Calculate Binding Free Energies of Phenylethanolamine N-Methyltransferase Inhibitors. ''J Chem Phys.'' 2011, submitted.<br />
<br />
2. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, '''Nair PC''', Oostenbrink C, Mark AE. An Automated force field Topology Builder (ATB) and repository: version 1.0. ''J Chem Theory Comput.'' 2011, submitted.<br />
<br />
3.'''Nair PC''', Malde AK, Mark AE."Using theory to reconcile experiment: the structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-MethylTransferase (PNMT)". ''J Chem Theory Comput.'' 2011, May;7(5):1458-1468 <br><br />
<br />
4.'''Nair PC'''. "Molecular Field Analysis (MFA) and other QSAR techniques in development of phosphatase inhibitors".<br />
''Anticancer Agents Med Chem.'' 2011 Jan;11(1):151-163. (Invited Review Article) <br><br />
<br />
5.'''Nair PC''', Sobhia ME. "Fingerprint directed scaffold hopping for identification of CCR2 antagonists".<br />
''J Chem Inf Model.'' 2008 Sep;48(9):1891-902. <br><br />
<br />
6.'''Nair PC''', Srikanth K, Sobhia ME. "QSAR studies on CCR2 antagonists with chiral sensitive hologram descriptors".<br />
''Bioorg Med Chem Lett.'' 2008 Feb 15;18(4):1323-30. <br><br />
<br />
7.Srikanth K, '''Nair PC''', Sobhia ME. "Probing the structural and topological requirements for CCR2 antagonism: holographic QSAR for <br> indolopiperidine derivatives".''Bioorg Med Chem Lett.'' 2008 Feb 15;18(4):1450-6. <br><br />
<br />
8.'''Nair PC''', Sobhia ME. "Comparative QSTR studies for predicting mutagenicity of nitro compounds".<br />
''J Mol Graph Model.'' 2008 Feb;26(6):916-34. <br><br />
<br />
9.'''Nair PC''', Sobhia ME. "Quantitative structure activity relationship studies on thiourea analogues as influenza virus neuraminidase inhibitors". ''Eur J Med Chem.'' 2008 Feb;43(2):293-9. <br><br />
<br />
10.'''Nair PC''', Sobhia ME."CoMFA based de novo design of pyridazine analogs as PTP1B inhibitors".<br />
''J Mol Graph Model.'' 2007 Jul;26(1):117-23. <br><br />
<br />
11.Khurana J, '''Nair P''',Sobhia ME. "Design of Allosteric Ligands Using Computer Aided Drug Design (CADD) Techniques", Current Research & Information on Pharmaceutical Sciences (CRIPS), 2006 Apr;7(2):8-13.(Review Article)<br><br />
<br />
== Poster Presentations ==<br />
1.'''Nair PC''', Malde AK, Mark AE."Validation of fragment hits in X-ray crystal complexes", The East Coast Protein Meeting, Coffs Harbour NSW, Australia, 15-17th July 2011<br />
<br />
2.'''Nair PC''', Malde AK, Mark AE."The structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-methyltransferase (PNMT): A Molecular Dynamics and Free Energy study", Molecular Modelling 2010, Melbourne, Australia, 28Nov-1Dec 2010.<br />
<br />
3.'''Nair PC''', Malde AK, Mark AE.Investigating structural requirements for PNMT inhibition: A molecular dynamics and free energy calculation study", Division of chemistry and structural biology symposium, Institute of Molecular Bioscience, Brisbane, Australia, Nov 18-19 2010.<br />
<br />
4.'''Nair PC''', Malde AK, Mark AE. "Investigation of ligand interaction and binding free Energy of 1,2,3,4 tetrahydroisoquinoline analogues as PNMT inhibitors", 61st Indian Pharmaceutical Congress, 11-13 December 2009.<br />
<br />
5.'''Nair PC''', Sobhia ME. "Identification of Novel CCR2 Scaffolds Through Fingerprint Directed Virtual Screening", Virtual Discovery Europe (Computer Aided Drug Design and Screening) London, England, 24-25 October 2007. (Presented by Dr. M. Elizabeth Sobhia, NIPER )<br />
<br />
6.'''Nair PC''', Sobhia ME. "Synergistic application of target structure based alignment and 3D-QSAR study of protein tyrosine phosphatases 1B (PTP1B) inhibitors", Workshop on Pharmcoinformatics: Tools for Drug Target Identification, NIPER, India, March 14-16, 2007.<br />
<br />
7.'''Nair PC''', Sobhia ME. "Quantitative Structure Toxicity Relationship (QSTR) Studies for Predicting Mutagenicity of Nitro Compounds", International Conference on Chemoinformatics, NCL, Pune, India, Jan 22, 2007.<br />
<br />
8.'''Nair PC''', Sobhia ME. "Design of novel PTP1B inhibitors using 3D-QSAR and concept of hypothetical cavity generation", Workshop on Pharmacoinformatics: QSAR, NIPER, India, March 3-4, 2006.<br />
<br />
== Other Conferences/Scientific visits ==<br />
<br />
Molecular Modelling (MM2009), Gold Coast, Queensland, Australia, July 26-29 2009. <br />
<br />
Attended 8th National Center of Competence in Research (NCCR) Practical Course in the area of computational structural biology, Kandersteg, Switzerland, Jan 10-15 2010.<br />
<br />
Visited as a scientific guest in the laboratory of Prof. Wilfred F. van Gunsteren, ETH Zurich, Switzerland, Jan 16-29 2010.<br />
<br />
== Contact Details ==<br />
<br />
Endeavour IPRS Doctoral Fellow <br><br />
Molecular Dynamics Group <br><br />
School of Chemistry and Molecular Biosciences (SCMB) <br><br />
Molecular Biosciences Building (#76) <br><br />
The University of Queensland <br><br />
St. Lucia Campus, Brisbane, QLD 4072 <br><br />
Australia <br><br />
<br />
'''email''' p.nair@uq.edu.au</div>PramodNairhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Pramod_Nair&diff=15936Pramod Nair2011-05-11T01:19:37Z<p>PramodNair: /* Publications */</p>
<hr />
<div>Automated Force Field Topology Builder (ATB) for GROMOS and GROMACS : MD group of Prof. Alan E. Mark<br />
http://compbio.biosci.uq.edu.au/atb/ <br />
<br />
== Research Interests ==<br />
Computer Aided Drug Design (CADD) and Free Energy Calculations<br />
<br />
Alternate Free energy methods to aid high-throughput virtual screening in drug discovery<br />
<br />
Molecular Dynamics simulations of macromolecular and small molecular systems<br />
<br />
== Academic ==<br />
'''B. Pharm.''' Bombay College of Pharmacy, University of Mumbai, India 2001-2005 <br><br />
'''MS (Pharm.)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2005-2007 <br><br />
'''Junior Research Fellow (JRF)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2007-2008 <br><br />
'''PhD Student''' Molecular Dynamics Group, School of Chemistry and Molecular Biosciences (SCMB),University of Queensland, Australia 2009 <br><br />
<br />
== Publications ==<br />
1. Riniker S, Christ CD, Hansen N, Mark AE, '''Nair PC''', van Gunsteren WF. Comparison of Enveloping Distribution Sampling and Thermodynamic Integration to Calculate Binding Free Energies of Phenylethanolamine N-Methyltransferase Inhibitors. ''J Chem Phys.'' 2011, submitted.<br />
<br />
2. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, '''Nair PC''', Oostenbrink C, Mark AE. An Automated force field Topology Builder (ATB) and repository: version 1.0. ''J Chem Theory Comput.'' 2011, submitted.<br />
<br />
3.'''Nair PC''', Malde AK, Mark AE."Using theory to reconcile experiment: the structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-MethylTransferase (PNMT)". ''J Chem Theory Comput.'' 2011, May;7(5):1458-1468 <br><br />
<br />
4.'''Nair PC'''. "Molecular Field Analysis (MFA) and other QSAR techniques in development of phosphatase inhibitors".<br />
''Anticancer Agents Med Chem.'' 2011 Jan;11(1):151-163. (Invited Review Article) <br><br />
<br />
5.'''Nair PC''', Sobhia ME. "Fingerprint directed scaffold hopping for identification of CCR2 antagonists".<br />
''J Chem Inf Model.'' 2008 Sep;48(9):1891-902. <br><br />
<br />
6.'''Nair PC''', Srikanth K, Sobhia ME. "QSAR studies on CCR2 antagonists with chiral sensitive hologram descriptors".<br />
''Bioorg Med Chem Lett.'' 2008 Feb 15;18(4):1323-30. <br><br />
<br />
7.Srikanth K, '''Nair PC''', Sobhia ME. "Probing the structural and topological requirements for CCR2 antagonism: holographic QSAR for <br> indolopiperidine derivatives".''Bioorg Med Chem Lett.'' 2008 Feb 15;18(4):1450-6. <br><br />
<br />
8.'''Nair PC''', Sobhia ME. "Comparative QSTR studies for predicting mutagenicity of nitro compounds".<br />
''J Mol Graph Model.'' 2008 Feb;26(6):916-34. <br><br />
<br />
9.'''Nair PC''', Sobhia ME. "Quantitative structure activity relationship studies on thiourea analogues as influenza virus neuraminidase inhibitors". ''Eur J Med Chem.'' 2008 Feb;43(2):293-9. <br><br />
<br />
10.'''Nair PC''', Sobhia ME."CoMFA based de novo design of pyridazine analogs as PTP1B inhibitors".<br />
''J Mol Graph Model.'' 2007 Jul;26(1):117-23. <br><br />
<br />
11.Khurana J, '''Nair P''',Sobhia ME. "Design of Allosteric Ligands Using Computer Aided Drug Design (CADD) Techniques", Current Research & Information on Pharmaceutical Sciences (CRIPS), 2006 Apr;7(2):8-13.(Review Article)<br><br />
<br />
== Poster Presentations ==<br />
1.'''Nair PC''', Malde AK, Mark AE."The structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-methyltransferase (PNMT): A Molecular Dynamics and Free Energy study", Molecular Modelling 2010, Melbourne, Australia, 28Nov-1Dec 2010.<br />
<br />
2.'''Nair PC''', Malde AK, Mark AE.Investigating structural requirements for PNMT inhibition: A molecular dynamics and free energy calculation study", Division of chemistry and structural biology symposium, Institute of Molecular Bioscience, Brisbane, Australia, Nov 18-19 2010.<br />
<br />
3.'''Nair PC''', Malde AK, Mark AE. "Investigation of ligand interaction and binding free Energy of 1,2,3,4 tetrahydroisoquinoline analogues as PNMT inhibitors", 61st Indian Pharmaceutical Congress, 11-13 December 2009.<br />
<br />
4.'''Nair PC''', Sobhia ME. "Identification of Novel CCR2 Scaffolds Through Fingerprint Directed Virtual Screening", Virtual Discovery Europe (Computer Aided Drug Design and Screening) London, England, 24-25 October 2007. (Presented by Dr. M. Elizabeth Sobhia, NIPER )<br />
<br />
5.'''Nair PC''', Sobhia ME. "Synergistic application of target structure based alignment and 3D-QSAR study of protein tyrosine phosphatases 1B (PTP1B) inhibitors", Workshop on Pharmcoinformatics: Tools for Drug Target Identification, NIPER, India, March 14-16, 2007.<br />
<br />
6.'''Nair PC''', Sobhia ME. "Quantitative Structure Toxicity Relationship (QSTR) Studies for Predicting Mutagenicity of Nitro Compounds", International Conference on Chemoinformatics, NCL, Pune, India, Jan 22, 2007.<br />
<br />
7.'''Nair PC''', Sobhia ME. "Design of novel PTP1B inhibitors using 3D-QSAR and concept of hypothetical cavity generation", Workshop on Pharmacoinformatics: QSAR, NIPER, India, March 3-4, 2006.<br />
<br />
== Other Conferences/Scientific visits ==<br />
<br />
Molecular Modelling (MM2009), Gold Coast, Queensland, Australia, July 26-29 2009. <br />
<br />
Attended 8th National Center of Competence in Research (NCCR) Practical Course in the area of computational structural biology, Kandersteg, Switzerland, Jan 10-15 2010.<br />
<br />
Visited as a scientific guest in the laboratory of Prof. Wilfred F. van Gunsteren, ETH Zurich, Switzerland, Jan 16-29 2010.<br />
<br />
== Contact Details ==<br />
<br />
Endeavour IPRS Doctoral Fellow <br><br />
Molecular Dynamics Group <br><br />
School of Chemistry and Molecular Biosciences (SCMB) <br><br />
Molecular Biosciences Building (#76) <br><br />
The University of Queensland <br><br />
St. Lucia Campus, Brisbane, QLD 4072 <br><br />
Australia <br><br />
<br />
'''email''' p.nair@uq.edu.au</div>PramodNairhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Pramod_Nair&diff=15925Pramod Nair2011-04-19T06:52:47Z<p>PramodNair: /* Publications */</p>
<hr />
<div>Automated Force Field Topology Builder (ATB) for GROMOS and GROMACS : MD group of Prof. Alan E. Mark<br />
http://compbio.biosci.uq.edu.au/atb/ <br />
<br />
== Research Interests ==<br />
Computer Aided Drug Design (CADD) and Free Energy Calculations<br />
<br />
Alternate Free energy methods to aid high-throughput virtual screening in drug discovery<br />
<br />
Molecular Dynamics simulations of macromolecular and small molecular systems<br />
<br />
== Academic ==<br />
'''B. Pharm.''' Bombay College of Pharmacy, University of Mumbai, India 2001-2005 <br><br />
'''MS (Pharm.)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2005-2007 <br><br />
'''Junior Research Fellow (JRF)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2007-2008 <br><br />
'''PhD Student''' Molecular Dynamics Group, School of Chemistry and Molecular Biosciences (SCMB),University of Queensland, Australia 2009 <br><br />
<br />
== Publications ==<br />
1. Riniker S, Christ CD, Hansen N, Mark AE, '''Nair PC''', van Gunsteren WF. Comparison of Enveloping Distribution Sampling and Thermodynamic Integration to Calculate Binding Free Energies of Phenylethanolamine N-Methyltransferase Inhibitors. ''J Chem Phys.'' 2011, submitted.<br />
<br />
2. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, '''Nair PC''', Oostenbrink C, Mark AE. An Automated force field Topology Builder (ATB) and repository: version 1.0. ''J Chem Theory Comput.'' 2011, submitted.<br />
<br />
3.'''Nair PC''', Malde AK, Mark AE."Using theory to reconcile experiment: the structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-MethylTransferase (PNMT)". ''J Chem Theory Comput.'' In press <br><br />
<br />
4.'''Nair PC'''. "Molecular Field Analysis (MFA) and other QSAR techniques in development of phosphatase inhibitors".<br />
''Anticancer Agents Med Chem.'' 2011 Jan;11(1):151-163. (Invited Review Article) <br><br />
<br />
5.'''Nair PC''', Sobhia ME. "Fingerprint directed scaffold hopping for identification of CCR2 antagonists".<br />
''J Chem Inf Model.'' 2008 Sep;48(9):1891-902. <br><br />
<br />
6.'''Nair PC''', Srikanth K, Sobhia ME. "QSAR studies on CCR2 antagonists with chiral sensitive hologram descriptors".<br />
''Bioorg Med Chem Lett.'' 2008 Feb 15;18(4):1323-30. <br><br />
<br />
7.Srikanth K, '''Nair PC''', Sobhia ME. "Probing the structural and topological requirements for CCR2 antagonism: holographic QSAR for <br> indolopiperidine derivatives".''Bioorg Med Chem Lett.'' 2008 Feb 15;18(4):1450-6. <br><br />
<br />
8.'''Nair PC''', Sobhia ME. "Comparative QSTR studies for predicting mutagenicity of nitro compounds".<br />
''J Mol Graph Model.'' 2008 Feb;26(6):916-34. <br><br />
<br />
9.'''Nair PC''', Sobhia ME. "Quantitative structure activity relationship studies on thiourea analogues as influenza virus neuraminidase inhibitors". ''Eur J Med Chem.'' 2008 Feb;43(2):293-9. <br><br />
<br />
10.'''Nair PC''', Sobhia ME."CoMFA based de novo design of pyridazine analogs as PTP1B inhibitors".<br />
''J Mol Graph Model.'' 2007 Jul;26(1):117-23. <br><br />
<br />
11.Khurana J, '''Nair P''',Sobhia ME. "Design of Allosteric Ligands Using Computer Aided Drug Design (CADD) Techniques", Current Research & Information on Pharmaceutical Sciences (CRIPS), 2006 Apr;7(2):8-13.(Review Article)<br><br />
<br />
== Poster Presentations ==<br />
1.'''Nair PC''', Malde AK, Mark AE."The structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-methyltransferase (PNMT): A Molecular Dynamics and Free Energy study", Molecular Modelling 2010, Melbourne, Australia, 28Nov-1Dec 2010.<br />
<br />
2.'''Nair PC''', Malde AK, Mark AE.Investigating structural requirements for PNMT inhibition: A molecular dynamics and free energy calculation study", Division of chemistry and structural biology symposium, Institute of Molecular Bioscience, Brisbane, Australia, Nov 18-19 2010.<br />
<br />
3.'''Nair PC''', Malde AK, Mark AE. "Investigation of ligand interaction and binding free Energy of 1,2,3,4 tetrahydroisoquinoline analogues as PNMT inhibitors", 61st Indian Pharmaceutical Congress, 11-13 December 2009.<br />
<br />
4.'''Nair PC''', Sobhia ME. "Identification of Novel CCR2 Scaffolds Through Fingerprint Directed Virtual Screening", Virtual Discovery Europe (Computer Aided Drug Design and Screening) London, England, 24-25 October 2007. (Presented by Dr. M. Elizabeth Sobhia, NIPER )<br />
<br />
5.'''Nair PC''', Sobhia ME. "Synergistic application of target structure based alignment and 3D-QSAR study of protein tyrosine phosphatases 1B (PTP1B) inhibitors", Workshop on Pharmcoinformatics: Tools for Drug Target Identification, NIPER, India, March 14-16, 2007.<br />
<br />
6.'''Nair PC''', Sobhia ME. "Quantitative Structure Toxicity Relationship (QSTR) Studies for Predicting Mutagenicity of Nitro Compounds", International Conference on Chemoinformatics, NCL, Pune, India, Jan 22, 2007.<br />
<br />
7.'''Nair PC''', Sobhia ME. "Design of novel PTP1B inhibitors using 3D-QSAR and concept of hypothetical cavity generation", Workshop on Pharmacoinformatics: QSAR, NIPER, India, March 3-4, 2006.<br />
<br />
== Other Conferences/Scientific visits ==<br />
<br />
Molecular Modelling (MM2009), Gold Coast, Queensland, Australia, July 26-29 2009. <br />
<br />
Attended 8th National Center of Competence in Research (NCCR) Practical Course in the area of computational structural biology, Kandersteg, Switzerland, Jan 10-15 2010.<br />
<br />
Visited as a scientific guest in the laboratory of Prof. Wilfred F. van Gunsteren, ETH Zurich, Switzerland, Jan 16-29 2010.<br />
<br />
== Contact Details ==<br />
<br />
Endeavour IPRS Doctoral Fellow <br><br />
Molecular Dynamics Group <br><br />
School of Chemistry and Molecular Biosciences (SCMB) <br><br />
Molecular Biosciences Building (#76) <br><br />
The University of Queensland <br><br />
St. Lucia Campus, Brisbane, QLD 4072 <br><br />
Australia <br><br />
<br />
'''email''' p.nair@uq.edu.au</div>PramodNairhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Pramod_Nair&diff=15924Pramod Nair2011-04-19T06:51:34Z<p>PramodNair: /* Publications */</p>
<hr />
<div>Automated Force Field Topology Builder (ATB) for GROMOS and GROMACS : MD group of Prof. Alan E. Mark<br />
http://compbio.biosci.uq.edu.au/atb/ <br />
<br />
== Research Interests ==<br />
Computer Aided Drug Design (CADD) and Free Energy Calculations<br />
<br />
Alternate Free energy methods to aid high-throughput virtual screening in drug discovery<br />
<br />
Molecular Dynamics simulations of macromolecular and small molecular systems<br />
<br />
== Academic ==<br />
'''B. Pharm.''' Bombay College of Pharmacy, University of Mumbai, India 2001-2005 <br><br />
'''MS (Pharm.)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2005-2007 <br><br />
'''Junior Research Fellow (JRF)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2007-2008 <br><br />
'''PhD Student''' Molecular Dynamics Group, School of Chemistry and Molecular Biosciences (SCMB),University of Queensland, Australia 2009 <br><br />
<br />
== Publications ==<br />
1. Riniker S, Christ CD, Hansen N, Mark AE, '''Nair PC''', van Gunsteren WF,Comparison of Enveloping Distribution Sampling and Thermodynamic Integration to Calculate Binding Free Energies of Phenylethanolamine N-Methyltransferase Inhibitors. ''J Chem Phys.'' 2011, submitted.<br />
<br />
2. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, '''Nair PC''', Oostenbrink C, Mark AE. An Automated force field Topology Builder (ATB) and repository: version 1.0. ''J Chem Theory Comput.'' 2011, submitted.<br />
<br />
3.'''Nair PC''', Malde AK, Mark AE."Using theory to reconcile experiment: the structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-MethylTransferase (PNMT)". ''J Chem Theory Comput.'' In press <br><br />
<br />
4.'''Nair PC'''. "Molecular Field Analysis (MFA) and other QSAR techniques in development of phosphatase inhibitors".<br />
''Anticancer Agents Med Chem.'' 2011 Jan;11(1):151-163. (Invited Review Article) <br><br />
<br />
5.'''Nair PC''', Sobhia ME. "Fingerprint directed scaffold hopping for identification of CCR2 antagonists".<br />
''J Chem Inf Model.'' 2008 Sep;48(9):1891-902. <br><br />
<br />
6.'''Nair PC''', Srikanth K, Sobhia ME. "QSAR studies on CCR2 antagonists with chiral sensitive hologram descriptors".<br />
''Bioorg Med Chem Lett.'' 2008 Feb 15;18(4):1323-30. <br><br />
<br />
7.Srikanth K, '''Nair PC''', Sobhia ME. "Probing the structural and topological requirements for CCR2 antagonism: holographic QSAR for <br> indolopiperidine derivatives".''Bioorg Med Chem Lett.'' 2008 Feb 15;18(4):1450-6. <br><br />
<br />
8.'''Nair PC''', Sobhia ME. "Comparative QSTR studies for predicting mutagenicity of nitro compounds".<br />
''J Mol Graph Model.'' 2008 Feb;26(6):916-34. <br><br />
<br />
9.'''Nair PC''', Sobhia ME. "Quantitative structure activity relationship studies on thiourea analogues as influenza virus neuraminidase inhibitors". ''Eur J Med Chem.'' 2008 Feb;43(2):293-9. <br><br />
<br />
10.'''Nair PC''', Sobhia ME."CoMFA based de novo design of pyridazine analogs as PTP1B inhibitors".<br />
''J Mol Graph Model.'' 2007 Jul;26(1):117-23. <br><br />
<br />
11.Khurana J, '''Nair P''',Sobhia ME. "Design of Allosteric Ligands Using Computer Aided Drug Design (CADD) Techniques", Current Research & Information on Pharmaceutical Sciences (CRIPS), 2006 Apr;7(2):8-13.(Review Article)<br><br />
<br />
== Poster Presentations ==<br />
1.'''Nair PC''', Malde AK, Mark AE."The structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-methyltransferase (PNMT): A Molecular Dynamics and Free Energy study", Molecular Modelling 2010, Melbourne, Australia, 28Nov-1Dec 2010.<br />
<br />
2.'''Nair PC''', Malde AK, Mark AE.Investigating structural requirements for PNMT inhibition: A molecular dynamics and free energy calculation study", Division of chemistry and structural biology symposium, Institute of Molecular Bioscience, Brisbane, Australia, Nov 18-19 2010.<br />
<br />
3.'''Nair PC''', Malde AK, Mark AE. "Investigation of ligand interaction and binding free Energy of 1,2,3,4 tetrahydroisoquinoline analogues as PNMT inhibitors", 61st Indian Pharmaceutical Congress, 11-13 December 2009.<br />
<br />
4.'''Nair PC''', Sobhia ME. "Identification of Novel CCR2 Scaffolds Through Fingerprint Directed Virtual Screening", Virtual Discovery Europe (Computer Aided Drug Design and Screening) London, England, 24-25 October 2007. (Presented by Dr. M. Elizabeth Sobhia, NIPER )<br />
<br />
5.'''Nair PC''', Sobhia ME. "Synergistic application of target structure based alignment and 3D-QSAR study of protein tyrosine phosphatases 1B (PTP1B) inhibitors", Workshop on Pharmcoinformatics: Tools for Drug Target Identification, NIPER, India, March 14-16, 2007.<br />
<br />
6.'''Nair PC''', Sobhia ME. "Quantitative Structure Toxicity Relationship (QSTR) Studies for Predicting Mutagenicity of Nitro Compounds", International Conference on Chemoinformatics, NCL, Pune, India, Jan 22, 2007.<br />
<br />
7.'''Nair PC''', Sobhia ME. "Design of novel PTP1B inhibitors using 3D-QSAR and concept of hypothetical cavity generation", Workshop on Pharmacoinformatics: QSAR, NIPER, India, March 3-4, 2006.<br />
<br />
== Other Conferences/Scientific visits ==<br />
<br />
Molecular Modelling (MM2009), Gold Coast, Queensland, Australia, July 26-29 2009. <br />
<br />
Attended 8th National Center of Competence in Research (NCCR) Practical Course in the area of computational structural biology, Kandersteg, Switzerland, Jan 10-15 2010.<br />
<br />
Visited as a scientific guest in the laboratory of Prof. Wilfred F. van Gunsteren, ETH Zurich, Switzerland, Jan 16-29 2010.<br />
<br />
== Contact Details ==<br />
<br />
Endeavour IPRS Doctoral Fellow <br><br />
Molecular Dynamics Group <br><br />
School of Chemistry and Molecular Biosciences (SCMB) <br><br />
Molecular Biosciences Building (#76) <br><br />
The University of Queensland <br><br />
St. Lucia Campus, Brisbane, QLD 4072 <br><br />
Australia <br><br />
<br />
'''email''' p.nair@uq.edu.au</div>PramodNairhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Pramod_Nair&diff=15922Pramod Nair2011-04-12T12:08:59Z<p>PramodNair: /* Research Interests */</p>
<hr />
<div>Automated Force Field Topology Builder (ATB) for GROMOS and GROMACS : MD group of Prof. Alan E. Mark<br />
http://compbio.biosci.uq.edu.au/atb/ <br />
<br />
== Research Interests ==<br />
Computer Aided Drug Design (CADD) and Free Energy Calculations<br />
<br />
Alternate Free energy methods to aid high-throughput virtual screening in drug discovery<br />
<br />
Molecular Dynamics simulations of macromolecular and small molecular systems<br />
<br />
== Academic ==<br />
'''B. Pharm.''' Bombay College of Pharmacy, University of Mumbai, India 2001-2005 <br><br />
'''MS (Pharm.)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2005-2007 <br><br />
'''Junior Research Fellow (JRF)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2007-2008 <br><br />
'''PhD Student''' Molecular Dynamics Group, School of Chemistry and Molecular Biosciences (SCMB),University of Queensland, Australia 2009 <br><br />
<br />
== Publications ==<br />
1. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, '''Nair PC''', Oostenbrink C, Mark AE. An Automated force field Topology Builder (ATB) and repository: version 1.0. ''J Chem Theory Comput.'' 2011, submitted.<br />
<br />
2.'''Nair PC''', Malde AK, Mark AE."Using theory to reconcile experiment: the structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-MethylTransferase (PNMT)". ''J Chem Theory Comput.'' In press <br><br />
<br />
3.'''Nair PC'''. "Molecular Field Analysis (MFA) and other QSAR techniques in development of phosphatase inhibitors".<br />
''Anticancer Agents Med Chem.'' 2011 Jan;11(1):151-163. (Invited Review Article) <br><br />
<br />
4.'''Nair PC''', Sobhia ME. "Fingerprint directed scaffold hopping for identification of CCR2 antagonists".<br />
''J Chem Inf Model.'' 2008 Sep;48(9):1891-902. <br><br />
<br />
5.'''Nair PC''', Srikanth K, Sobhia ME. "QSAR studies on CCR2 antagonists with chiral sensitive hologram descriptors".<br />
''Bioorg Med Chem Lett.'' 2008 Feb 15;18(4):1323-30. <br><br />
<br />
6.Srikanth K, '''Nair PC''', Sobhia ME. "Probing the structural and topological requirements for CCR2 antagonism: holographic QSAR for <br> indolopiperidine derivatives".''Bioorg Med Chem Lett.'' 2008 Feb 15;18(4):1450-6. <br><br />
<br />
7.'''Nair PC''', Sobhia ME. "Comparative QSTR studies for predicting mutagenicity of nitro compounds".<br />
''J Mol Graph Model.'' 2008 Feb;26(6):916-34. <br><br />
<br />
8.'''Nair PC''', Sobhia ME. "Quantitative structure activity relationship studies on thiourea analogues as influenza virus neuraminidase inhibitors". ''Eur J Med Chem.'' 2008 Feb;43(2):293-9. <br><br />
<br />
9.'''Nair PC''', Sobhia ME."CoMFA based de novo design of pyridazine analogs as PTP1B inhibitors".<br />
''J Mol Graph Model.'' 2007 Jul;26(1):117-23. <br><br />
<br />
10.Khurana J, '''Nair P''',Sobhia ME. "Design of Allosteric Ligands Using Computer Aided Drug Design (CADD) Techniques", Current Research & Information on Pharmaceutical Sciences (CRIPS), 2006 Apr;7(2):8-13.(Review Article)<br><br />
<br />
== Poster Presentations ==<br />
1.'''Nair PC''', Malde AK, Mark AE."The structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-methyltransferase (PNMT): A Molecular Dynamics and Free Energy study", Molecular Modelling 2010, Melbourne, Australia, 28Nov-1Dec 2010.<br />
<br />
2.'''Nair PC''', Malde AK, Mark AE.Investigating structural requirements for PNMT inhibition: A molecular dynamics and free energy calculation study", Division of chemistry and structural biology symposium, Institute of Molecular Bioscience, Brisbane, Australia, Nov 18-19 2010.<br />
<br />
3.'''Nair PC''', Malde AK, Mark AE. "Investigation of ligand interaction and binding free Energy of 1,2,3,4 tetrahydroisoquinoline analogues as PNMT inhibitors", 61st Indian Pharmaceutical Congress, 11-13 December 2009.<br />
<br />
4.'''Nair PC''', Sobhia ME. "Identification of Novel CCR2 Scaffolds Through Fingerprint Directed Virtual Screening", Virtual Discovery Europe (Computer Aided Drug Design and Screening) London, England, 24-25 October 2007. (Presented by Dr. M. Elizabeth Sobhia, NIPER )<br />
<br />
5.'''Nair PC''', Sobhia ME. "Synergistic application of target structure based alignment and 3D-QSAR study of protein tyrosine phosphatases 1B (PTP1B) inhibitors", Workshop on Pharmcoinformatics: Tools for Drug Target Identification, NIPER, India, March 14-16, 2007.<br />
<br />
6.'''Nair PC''', Sobhia ME. "Quantitative Structure Toxicity Relationship (QSTR) Studies for Predicting Mutagenicity of Nitro Compounds", International Conference on Chemoinformatics, NCL, Pune, India, Jan 22, 2007.<br />
<br />
7.'''Nair PC''', Sobhia ME. "Design of novel PTP1B inhibitors using 3D-QSAR and concept of hypothetical cavity generation", Workshop on Pharmacoinformatics: QSAR, NIPER, India, March 3-4, 2006.<br />
<br />
== Other Conferences/Scientific visits ==<br />
<br />
Molecular Modelling (MM2009), Gold Coast, Queensland, Australia, July 26-29 2009. <br />
<br />
Attended 8th National Center of Competence in Research (NCCR) Practical Course in the area of computational structural biology, Kandersteg, Switzerland, Jan 10-15 2010.<br />
<br />
Visited as a scientific guest in the laboratory of Prof. Wilfred F. van Gunsteren, ETH Zurich, Switzerland, Jan 16-29 2010.<br />
<br />
== Contact Details ==<br />
<br />
Endeavour IPRS Doctoral Fellow <br><br />
Molecular Dynamics Group <br><br />
School of Chemistry and Molecular Biosciences (SCMB) <br><br />
Molecular Biosciences Building (#76) <br><br />
The University of Queensland <br><br />
St. Lucia Campus, Brisbane, QLD 4072 <br><br />
Australia <br><br />
<br />
'''email''' p.nair@uq.edu.au</div>PramodNairhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=File:DSC_0127.jpg&diff=15921File:DSC 0127.jpg2011-04-12T12:08:24Z<p>PramodNair: </p>
<hr />
<div></div>PramodNairhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Pramod_Nair&diff=15920Pramod Nair2011-04-12T12:08:01Z<p>PramodNair: /* Research Interests */</p>
<hr />
<div>Automated Force Field Topology Builder (ATB) for GROMOS and GROMACS : MD group of Prof. Alan E. Mark<br />
http://compbio.biosci.uq.edu.au/atb/ <br />
<br />
== Research Interests ==<br />
Computer Aided Drug Design (CADD) and Free Energy Calculations<br />
<br />
Alternate Free energy methods to aid high-throughput virtual screening in drug discovery<br />
<br />
Molecular Dynamics simulations of macromolecular and small molecular systems<br />
<br />
[[Image:DSC_0127.jpg|50px|]]<br />
<br />
== Academic ==<br />
'''B. Pharm.''' Bombay College of Pharmacy, University of Mumbai, India 2001-2005 <br><br />
'''MS (Pharm.)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2005-2007 <br><br />
'''Junior Research Fellow (JRF)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2007-2008 <br><br />
'''PhD Student''' Molecular Dynamics Group, School of Chemistry and Molecular Biosciences (SCMB),University of Queensland, Australia 2009 <br><br />
<br />
== Publications ==<br />
1. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, '''Nair PC''', Oostenbrink C, Mark AE. An Automated force field Topology Builder (ATB) and repository: version 1.0. ''J Chem Theory Comput.'' 2011, submitted.<br />
<br />
2.'''Nair PC''', Malde AK, Mark AE."Using theory to reconcile experiment: the structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-MethylTransferase (PNMT)". ''J Chem Theory Comput.'' In press <br><br />
<br />
3.'''Nair PC'''. "Molecular Field Analysis (MFA) and other QSAR techniques in development of phosphatase inhibitors".<br />
''Anticancer Agents Med Chem.'' 2011 Jan;11(1):151-163. (Invited Review Article) <br><br />
<br />
4.'''Nair PC''', Sobhia ME. "Fingerprint directed scaffold hopping for identification of CCR2 antagonists".<br />
''J Chem Inf Model.'' 2008 Sep;48(9):1891-902. <br><br />
<br />
5.'''Nair PC''', Srikanth K, Sobhia ME. "QSAR studies on CCR2 antagonists with chiral sensitive hologram descriptors".<br />
''Bioorg Med Chem Lett.'' 2008 Feb 15;18(4):1323-30. <br><br />
<br />
6.Srikanth K, '''Nair PC''', Sobhia ME. "Probing the structural and topological requirements for CCR2 antagonism: holographic QSAR for <br> indolopiperidine derivatives".''Bioorg Med Chem Lett.'' 2008 Feb 15;18(4):1450-6. <br><br />
<br />
7.'''Nair PC''', Sobhia ME. "Comparative QSTR studies for predicting mutagenicity of nitro compounds".<br />
''J Mol Graph Model.'' 2008 Feb;26(6):916-34. <br><br />
<br />
8.'''Nair PC''', Sobhia ME. "Quantitative structure activity relationship studies on thiourea analogues as influenza virus neuraminidase inhibitors". ''Eur J Med Chem.'' 2008 Feb;43(2):293-9. <br><br />
<br />
9.'''Nair PC''', Sobhia ME."CoMFA based de novo design of pyridazine analogs as PTP1B inhibitors".<br />
''J Mol Graph Model.'' 2007 Jul;26(1):117-23. <br><br />
<br />
10.Khurana J, '''Nair P''',Sobhia ME. "Design of Allosteric Ligands Using Computer Aided Drug Design (CADD) Techniques", Current Research & Information on Pharmaceutical Sciences (CRIPS), 2006 Apr;7(2):8-13.(Review Article)<br><br />
<br />
== Poster Presentations ==<br />
1.'''Nair PC''', Malde AK, Mark AE."The structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-methyltransferase (PNMT): A Molecular Dynamics and Free Energy study", Molecular Modelling 2010, Melbourne, Australia, 28Nov-1Dec 2010.<br />
<br />
2.'''Nair PC''', Malde AK, Mark AE.Investigating structural requirements for PNMT inhibition: A molecular dynamics and free energy calculation study", Division of chemistry and structural biology symposium, Institute of Molecular Bioscience, Brisbane, Australia, Nov 18-19 2010.<br />
<br />
3.'''Nair PC''', Malde AK, Mark AE. "Investigation of ligand interaction and binding free Energy of 1,2,3,4 tetrahydroisoquinoline analogues as PNMT inhibitors", 61st Indian Pharmaceutical Congress, 11-13 December 2009.<br />
<br />
4.'''Nair PC''', Sobhia ME. "Identification of Novel CCR2 Scaffolds Through Fingerprint Directed Virtual Screening", Virtual Discovery Europe (Computer Aided Drug Design and Screening) London, England, 24-25 October 2007. (Presented by Dr. M. Elizabeth Sobhia, NIPER )<br />
<br />
5.'''Nair PC''', Sobhia ME. "Synergistic application of target structure based alignment and 3D-QSAR study of protein tyrosine phosphatases 1B (PTP1B) inhibitors", Workshop on Pharmcoinformatics: Tools for Drug Target Identification, NIPER, India, March 14-16, 2007.<br />
<br />
6.'''Nair PC''', Sobhia ME. "Quantitative Structure Toxicity Relationship (QSTR) Studies for Predicting Mutagenicity of Nitro Compounds", International Conference on Chemoinformatics, NCL, Pune, India, Jan 22, 2007.<br />
<br />
7.'''Nair PC''', Sobhia ME. "Design of novel PTP1B inhibitors using 3D-QSAR and concept of hypothetical cavity generation", Workshop on Pharmacoinformatics: QSAR, NIPER, India, March 3-4, 2006.<br />
<br />
== Other Conferences/Scientific visits ==<br />
<br />
Molecular Modelling (MM2009), Gold Coast, Queensland, Australia, July 26-29 2009. <br />
<br />
Attended 8th National Center of Competence in Research (NCCR) Practical Course in the area of computational structural biology, Kandersteg, Switzerland, Jan 10-15 2010.<br />
<br />
Visited as a scientific guest in the laboratory of Prof. Wilfred F. van Gunsteren, ETH Zurich, Switzerland, Jan 16-29 2010.<br />
<br />
== Contact Details ==<br />
<br />
Endeavour IPRS Doctoral Fellow <br><br />
Molecular Dynamics Group <br><br />
School of Chemistry and Molecular Biosciences (SCMB) <br><br />
Molecular Biosciences Building (#76) <br><br />
The University of Queensland <br><br />
St. Lucia Campus, Brisbane, QLD 4072 <br><br />
Australia <br><br />
<br />
'''email''' p.nair@uq.edu.au</div>PramodNairhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Pramod_Nair&diff=15919Pramod Nair2011-04-12T12:06:55Z<p>PramodNair: /* Research Interests */</p>
<hr />
<div>Automated Force Field Topology Builder (ATB) for GROMOS and GROMACS : MD group of Prof. Alan E. Mark<br />
http://compbio.biosci.uq.edu.au/atb/ <br />
<br />
== Research Interests ==<br />
Computer Aided Drug Design (CADD) and Free Energy Calculations<br />
<br />
Alternate Free energy methods to aid high-throughput virtual screening in drug discovery<br />
<br />
Molecular Dynamics simulations of macromolecular and small molecular systems<br />
<br />
[[Image:DSC_0127.jpeg|50px|]]<br />
<br />
== Academic ==<br />
'''B. Pharm.''' Bombay College of Pharmacy, University of Mumbai, India 2001-2005 <br><br />
'''MS (Pharm.)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2005-2007 <br><br />
'''Junior Research Fellow (JRF)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2007-2008 <br><br />
'''PhD Student''' Molecular Dynamics Group, School of Chemistry and Molecular Biosciences (SCMB),University of Queensland, Australia 2009 <br><br />
<br />
== Publications ==<br />
1. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, '''Nair PC''', Oostenbrink C, Mark AE. An Automated force field Topology Builder (ATB) and repository: version 1.0. ''J Chem Theory Comput.'' 2011, submitted.<br />
<br />
2.'''Nair PC''', Malde AK, Mark AE."Using theory to reconcile experiment: the structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-MethylTransferase (PNMT)". ''J Chem Theory Comput.'' In press <br><br />
<br />
3.'''Nair PC'''. "Molecular Field Analysis (MFA) and other QSAR techniques in development of phosphatase inhibitors".<br />
''Anticancer Agents Med Chem.'' 2011 Jan;11(1):151-163. (Invited Review Article) <br><br />
<br />
4.'''Nair PC''', Sobhia ME. "Fingerprint directed scaffold hopping for identification of CCR2 antagonists".<br />
''J Chem Inf Model.'' 2008 Sep;48(9):1891-902. <br><br />
<br />
5.'''Nair PC''', Srikanth K, Sobhia ME. "QSAR studies on CCR2 antagonists with chiral sensitive hologram descriptors".<br />
''Bioorg Med Chem Lett.'' 2008 Feb 15;18(4):1323-30. <br><br />
<br />
6.Srikanth K, '''Nair PC''', Sobhia ME. "Probing the structural and topological requirements for CCR2 antagonism: holographic QSAR for <br> indolopiperidine derivatives".''Bioorg Med Chem Lett.'' 2008 Feb 15;18(4):1450-6. <br><br />
<br />
7.'''Nair PC''', Sobhia ME. "Comparative QSTR studies for predicting mutagenicity of nitro compounds".<br />
''J Mol Graph Model.'' 2008 Feb;26(6):916-34. <br><br />
<br />
8.'''Nair PC''', Sobhia ME. "Quantitative structure activity relationship studies on thiourea analogues as influenza virus neuraminidase inhibitors". ''Eur J Med Chem.'' 2008 Feb;43(2):293-9. <br><br />
<br />
9.'''Nair PC''', Sobhia ME."CoMFA based de novo design of pyridazine analogs as PTP1B inhibitors".<br />
''J Mol Graph Model.'' 2007 Jul;26(1):117-23. <br><br />
<br />
10.Khurana J, '''Nair P''',Sobhia ME. "Design of Allosteric Ligands Using Computer Aided Drug Design (CADD) Techniques", Current Research & Information on Pharmaceutical Sciences (CRIPS), 2006 Apr;7(2):8-13.(Review Article)<br><br />
<br />
== Poster Presentations ==<br />
1.'''Nair PC''', Malde AK, Mark AE."The structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-methyltransferase (PNMT): A Molecular Dynamics and Free Energy study", Molecular Modelling 2010, Melbourne, Australia, 28Nov-1Dec 2010.<br />
<br />
2.'''Nair PC''', Malde AK, Mark AE.Investigating structural requirements for PNMT inhibition: A molecular dynamics and free energy calculation study", Division of chemistry and structural biology symposium, Institute of Molecular Bioscience, Brisbane, Australia, Nov 18-19 2010.<br />
<br />
3.'''Nair PC''', Malde AK, Mark AE. "Investigation of ligand interaction and binding free Energy of 1,2,3,4 tetrahydroisoquinoline analogues as PNMT inhibitors", 61st Indian Pharmaceutical Congress, 11-13 December 2009.<br />
<br />
4.'''Nair PC''', Sobhia ME. "Identification of Novel CCR2 Scaffolds Through Fingerprint Directed Virtual Screening", Virtual Discovery Europe (Computer Aided Drug Design and Screening) London, England, 24-25 October 2007. (Presented by Dr. M. Elizabeth Sobhia, NIPER )<br />
<br />
5.'''Nair PC''', Sobhia ME. "Synergistic application of target structure based alignment and 3D-QSAR study of protein tyrosine phosphatases 1B (PTP1B) inhibitors", Workshop on Pharmcoinformatics: Tools for Drug Target Identification, NIPER, India, March 14-16, 2007.<br />
<br />
6.'''Nair PC''', Sobhia ME. "Quantitative Structure Toxicity Relationship (QSTR) Studies for Predicting Mutagenicity of Nitro Compounds", International Conference on Chemoinformatics, NCL, Pune, India, Jan 22, 2007.<br />
<br />
7.'''Nair PC''', Sobhia ME. "Design of novel PTP1B inhibitors using 3D-QSAR and concept of hypothetical cavity generation", Workshop on Pharmacoinformatics: QSAR, NIPER, India, March 3-4, 2006.<br />
<br />
== Other Conferences/Scientific visits ==<br />
<br />
Molecular Modelling (MM2009), Gold Coast, Queensland, Australia, July 26-29 2009. <br />
<br />
Attended 8th National Center of Competence in Research (NCCR) Practical Course in the area of computational structural biology, Kandersteg, Switzerland, Jan 10-15 2010.<br />
<br />
Visited as a scientific guest in the laboratory of Prof. Wilfred F. van Gunsteren, ETH Zurich, Switzerland, Jan 16-29 2010.<br />
<br />
== Contact Details ==<br />
<br />
Endeavour IPRS Doctoral Fellow <br><br />
Molecular Dynamics Group <br><br />
School of Chemistry and Molecular Biosciences (SCMB) <br><br />
Molecular Biosciences Building (#76) <br><br />
The University of Queensland <br><br />
St. Lucia Campus, Brisbane, QLD 4072 <br><br />
Australia <br><br />
<br />
'''email''' p.nair@uq.edu.au</div>PramodNairhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Pramod_Nair&diff=15918Pramod Nair2011-04-12T12:04:36Z<p>PramodNair: /* Research Interests */</p>
<hr />
<div>Automated Force Field Topology Builder (ATB) for GROMOS and GROMACS : MD group of Prof. Alan E. Mark<br />
http://compbio.biosci.uq.edu.au/atb/ <br />
<br />
== Research Interests ==<br />
Computer Aided Drug Design (CADD) and Free Energy Calculations<br />
<br />
Alternate Free energy methods to aid high-throughput virtual screening in drug discovery<br />
<br />
Molecular Dynamics simulations of macromolecular and small molecular systems<br />
<br />
== Academic ==<br />
'''B. Pharm.''' Bombay College of Pharmacy, University of Mumbai, India 2001-2005 <br><br />
'''MS (Pharm.)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2005-2007 <br><br />
'''Junior Research Fellow (JRF)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2007-2008 <br><br />
'''PhD Student''' Molecular Dynamics Group, School of Chemistry and Molecular Biosciences (SCMB),University of Queensland, Australia 2009 <br><br />
<br />
== Publications ==<br />
1. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, '''Nair PC''', Oostenbrink C, Mark AE. An Automated force field Topology Builder (ATB) and repository: version 1.0. ''J Chem Theory Comput.'' 2011, submitted.<br />
<br />
2.'''Nair PC''', Malde AK, Mark AE."Using theory to reconcile experiment: the structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-MethylTransferase (PNMT)". ''J Chem Theory Comput.'' In press <br><br />
<br />
3.'''Nair PC'''. "Molecular Field Analysis (MFA) and other QSAR techniques in development of phosphatase inhibitors".<br />
''Anticancer Agents Med Chem.'' 2011 Jan;11(1):151-163. (Invited Review Article) <br><br />
<br />
4.'''Nair PC''', Sobhia ME. "Fingerprint directed scaffold hopping for identification of CCR2 antagonists".<br />
''J Chem Inf Model.'' 2008 Sep;48(9):1891-902. <br><br />
<br />
5.'''Nair PC''', Srikanth K, Sobhia ME. "QSAR studies on CCR2 antagonists with chiral sensitive hologram descriptors".<br />
''Bioorg Med Chem Lett.'' 2008 Feb 15;18(4):1323-30. <br><br />
<br />
6.Srikanth K, '''Nair PC''', Sobhia ME. "Probing the structural and topological requirements for CCR2 antagonism: holographic QSAR for <br> indolopiperidine derivatives".''Bioorg Med Chem Lett.'' 2008 Feb 15;18(4):1450-6. <br><br />
<br />
7.'''Nair PC''', Sobhia ME. "Comparative QSTR studies for predicting mutagenicity of nitro compounds".<br />
''J Mol Graph Model.'' 2008 Feb;26(6):916-34. <br><br />
<br />
8.'''Nair PC''', Sobhia ME. "Quantitative structure activity relationship studies on thiourea analogues as influenza virus neuraminidase inhibitors". ''Eur J Med Chem.'' 2008 Feb;43(2):293-9. <br><br />
<br />
9.'''Nair PC''', Sobhia ME."CoMFA based de novo design of pyridazine analogs as PTP1B inhibitors".<br />
''J Mol Graph Model.'' 2007 Jul;26(1):117-23. <br><br />
<br />
10.Khurana J, '''Nair P''',Sobhia ME. "Design of Allosteric Ligands Using Computer Aided Drug Design (CADD) Techniques", Current Research & Information on Pharmaceutical Sciences (CRIPS), 2006 Apr;7(2):8-13.(Review Article)<br><br />
<br />
== Poster Presentations ==<br />
1.'''Nair PC''', Malde AK, Mark AE."The structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-methyltransferase (PNMT): A Molecular Dynamics and Free Energy study", Molecular Modelling 2010, Melbourne, Australia, 28Nov-1Dec 2010.<br />
<br />
2.'''Nair PC''', Malde AK, Mark AE.Investigating structural requirements for PNMT inhibition: A molecular dynamics and free energy calculation study", Division of chemistry and structural biology symposium, Institute of Molecular Bioscience, Brisbane, Australia, Nov 18-19 2010.<br />
<br />
3.'''Nair PC''', Malde AK, Mark AE. "Investigation of ligand interaction and binding free Energy of 1,2,3,4 tetrahydroisoquinoline analogues as PNMT inhibitors", 61st Indian Pharmaceutical Congress, 11-13 December 2009.<br />
<br />
4.'''Nair PC''', Sobhia ME. "Identification of Novel CCR2 Scaffolds Through Fingerprint Directed Virtual Screening", Virtual Discovery Europe (Computer Aided Drug Design and Screening) London, England, 24-25 October 2007. (Presented by Dr. M. Elizabeth Sobhia, NIPER )<br />
<br />
5.'''Nair PC''', Sobhia ME. "Synergistic application of target structure based alignment and 3D-QSAR study of protein tyrosine phosphatases 1B (PTP1B) inhibitors", Workshop on Pharmcoinformatics: Tools for Drug Target Identification, NIPER, India, March 14-16, 2007.<br />
<br />
6.'''Nair PC''', Sobhia ME. "Quantitative Structure Toxicity Relationship (QSTR) Studies for Predicting Mutagenicity of Nitro Compounds", International Conference on Chemoinformatics, NCL, Pune, India, Jan 22, 2007.<br />
<br />
7.'''Nair PC''', Sobhia ME. "Design of novel PTP1B inhibitors using 3D-QSAR and concept of hypothetical cavity generation", Workshop on Pharmacoinformatics: QSAR, NIPER, India, March 3-4, 2006.<br />
<br />
== Other Conferences/Scientific visits ==<br />
<br />
Molecular Modelling (MM2009), Gold Coast, Queensland, Australia, July 26-29 2009. <br />
<br />
Attended 8th National Center of Competence in Research (NCCR) Practical Course in the area of computational structural biology, Kandersteg, Switzerland, Jan 10-15 2010.<br />
<br />
Visited as a scientific guest in the laboratory of Prof. Wilfred F. van Gunsteren, ETH Zurich, Switzerland, Jan 16-29 2010.<br />
<br />
== Contact Details ==<br />
<br />
Endeavour IPRS Doctoral Fellow <br><br />
Molecular Dynamics Group <br><br />
School of Chemistry and Molecular Biosciences (SCMB) <br><br />
Molecular Biosciences Building (#76) <br><br />
The University of Queensland <br><br />
St. Lucia Campus, Brisbane, QLD 4072 <br><br />
Australia <br><br />
<br />
'''email''' p.nair@uq.edu.au</div>PramodNairhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=File:DSC_0127.jpeg&diff=15917File:DSC 0127.jpeg2011-04-12T12:03:34Z<p>PramodNair: </p>
<hr />
<div></div>PramodNairhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Pramod_Nair&diff=15916Pramod Nair2011-04-12T12:02:58Z<p>PramodNair: /* Research Interests */</p>
<hr />
<div>Automated Force Field Topology Builder (ATB) for GROMOS and GROMACS : MD group of Prof. Alan E. Mark<br />
http://compbio.biosci.uq.edu.au/atb/ <br />
<br />
== Research Interests ==<br />
Computer Aided Drug Design (CADD) and Free Energy Calculations<br />
<br />
Alternate Free energy methods to aid high-throughput virtual screening in drug discovery<br />
<br />
Molecular Dynamics simulations of macromolecular and small molecular systems<br />
[[Image:DSC_0127.jpeg]]<br />
<br />
== Academic ==<br />
'''B. Pharm.''' Bombay College of Pharmacy, University of Mumbai, India 2001-2005 <br><br />
'''MS (Pharm.)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2005-2007 <br><br />
'''Junior Research Fellow (JRF)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2007-2008 <br><br />
'''PhD Student''' Molecular Dynamics Group, School of Chemistry and Molecular Biosciences (SCMB),University of Queensland, Australia 2009 <br><br />
<br />
== Publications ==<br />
1. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, '''Nair PC''', Oostenbrink C, Mark AE. An Automated force field Topology Builder (ATB) and repository: version 1.0. ''J Chem Theory Comput.'' 2011, submitted.<br />
<br />
2.'''Nair PC''', Malde AK, Mark AE."Using theory to reconcile experiment: the structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-MethylTransferase (PNMT)". ''J Chem Theory Comput.'' In press <br><br />
<br />
3.'''Nair PC'''. "Molecular Field Analysis (MFA) and other QSAR techniques in development of phosphatase inhibitors".<br />
''Anticancer Agents Med Chem.'' 2011 Jan;11(1):151-163. (Invited Review Article) <br><br />
<br />
4.'''Nair PC''', Sobhia ME. "Fingerprint directed scaffold hopping for identification of CCR2 antagonists".<br />
''J Chem Inf Model.'' 2008 Sep;48(9):1891-902. <br><br />
<br />
5.'''Nair PC''', Srikanth K, Sobhia ME. "QSAR studies on CCR2 antagonists with chiral sensitive hologram descriptors".<br />
''Bioorg Med Chem Lett.'' 2008 Feb 15;18(4):1323-30. <br><br />
<br />
6.Srikanth K, '''Nair PC''', Sobhia ME. "Probing the structural and topological requirements for CCR2 antagonism: holographic QSAR for <br> indolopiperidine derivatives".''Bioorg Med Chem Lett.'' 2008 Feb 15;18(4):1450-6. <br><br />
<br />
7.'''Nair PC''', Sobhia ME. "Comparative QSTR studies for predicting mutagenicity of nitro compounds".<br />
''J Mol Graph Model.'' 2008 Feb;26(6):916-34. <br><br />
<br />
8.'''Nair PC''', Sobhia ME. "Quantitative structure activity relationship studies on thiourea analogues as influenza virus neuraminidase inhibitors". ''Eur J Med Chem.'' 2008 Feb;43(2):293-9. <br><br />
<br />
9.'''Nair PC''', Sobhia ME."CoMFA based de novo design of pyridazine analogs as PTP1B inhibitors".<br />
''J Mol Graph Model.'' 2007 Jul;26(1):117-23. <br><br />
<br />
10.Khurana J, '''Nair P''',Sobhia ME. "Design of Allosteric Ligands Using Computer Aided Drug Design (CADD) Techniques", Current Research & Information on Pharmaceutical Sciences (CRIPS), 2006 Apr;7(2):8-13.(Review Article)<br><br />
<br />
== Poster Presentations ==<br />
1.'''Nair PC''', Malde AK, Mark AE."The structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-methyltransferase (PNMT): A Molecular Dynamics and Free Energy study", Molecular Modelling 2010, Melbourne, Australia, 28Nov-1Dec 2010.<br />
<br />
2.'''Nair PC''', Malde AK, Mark AE.Investigating structural requirements for PNMT inhibition: A molecular dynamics and free energy calculation study", Division of chemistry and structural biology symposium, Institute of Molecular Bioscience, Brisbane, Australia, Nov 18-19 2010.<br />
<br />
3.'''Nair PC''', Malde AK, Mark AE. "Investigation of ligand interaction and binding free Energy of 1,2,3,4 tetrahydroisoquinoline analogues as PNMT inhibitors", 61st Indian Pharmaceutical Congress, 11-13 December 2009.<br />
<br />
4.'''Nair PC''', Sobhia ME. "Identification of Novel CCR2 Scaffolds Through Fingerprint Directed Virtual Screening", Virtual Discovery Europe (Computer Aided Drug Design and Screening) London, England, 24-25 October 2007. (Presented by Dr. M. Elizabeth Sobhia, NIPER )<br />
<br />
5.'''Nair PC''', Sobhia ME. "Synergistic application of target structure based alignment and 3D-QSAR study of protein tyrosine phosphatases 1B (PTP1B) inhibitors", Workshop on Pharmcoinformatics: Tools for Drug Target Identification, NIPER, India, March 14-16, 2007.<br />
<br />
6.'''Nair PC''', Sobhia ME. "Quantitative Structure Toxicity Relationship (QSTR) Studies for Predicting Mutagenicity of Nitro Compounds", International Conference on Chemoinformatics, NCL, Pune, India, Jan 22, 2007.<br />
<br />
7.'''Nair PC''', Sobhia ME. "Design of novel PTP1B inhibitors using 3D-QSAR and concept of hypothetical cavity generation", Workshop on Pharmacoinformatics: QSAR, NIPER, India, March 3-4, 2006.<br />
<br />
== Other Conferences/Scientific visits ==<br />
<br />
Molecular Modelling (MM2009), Gold Coast, Queensland, Australia, July 26-29 2009. <br />
<br />
Attended 8th National Center of Competence in Research (NCCR) Practical Course in the area of computational structural biology, Kandersteg, Switzerland, Jan 10-15 2010.<br />
<br />
Visited as a scientific guest in the laboratory of Prof. Wilfred F. van Gunsteren, ETH Zurich, Switzerland, Jan 16-29 2010.<br />
<br />
== Contact Details ==<br />
<br />
Endeavour IPRS Doctoral Fellow <br><br />
Molecular Dynamics Group <br><br />
School of Chemistry and Molecular Biosciences (SCMB) <br><br />
Molecular Biosciences Building (#76) <br><br />
The University of Queensland <br><br />
St. Lucia Campus, Brisbane, QLD 4072 <br><br />
Australia <br><br />
<br />
'''email''' p.nair@uq.edu.au</div>PramodNairhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=File:Test.jpg&diff=15915File:Test.jpg2011-04-12T12:01:11Z<p>PramodNair: uploaded a new version of "Image:Test.jpg"</p>
<hr />
<div></div>PramodNairhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Pramod_Nair&diff=15914Pramod Nair2011-04-12T11:57:07Z<p>PramodNair: /* Research Interests */</p>
<hr />
<div>Automated Force Field Topology Builder (ATB) for GROMOS and GROMACS : MD group of Prof. Alan E. Mark<br />
http://compbio.biosci.uq.edu.au/atb/ <br />
<br />
== Research Interests ==<br />
Computer Aided Drug Design (CADD) and Free Energy Calculations<br />
<br />
Alternate Free energy methods to aid high-throughput virtual screening in drug discovery<br />
<br />
Molecular Dynamics simulations of macromolecular and small molecular systems<br />
[[Image:test.jpeg]]<br />
<br />
== Academic ==<br />
'''B. Pharm.''' Bombay College of Pharmacy, University of Mumbai, India 2001-2005 <br><br />
'''MS (Pharm.)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2005-2007 <br><br />
'''Junior Research Fellow (JRF)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2007-2008 <br><br />
'''PhD Student''' Molecular Dynamics Group, School of Chemistry and Molecular Biosciences (SCMB),University of Queensland, Australia 2009 <br><br />
<br />
== Publications ==<br />
1. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, '''Nair PC''', Oostenbrink C, Mark AE. An Automated force field Topology Builder (ATB) and repository: version 1.0. ''J Chem Theory Comput.'' 2011, submitted.<br />
<br />
2.'''Nair PC''', Malde AK, Mark AE."Using theory to reconcile experiment: the structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-MethylTransferase (PNMT)". ''J Chem Theory Comput.'' In press <br><br />
<br />
3.'''Nair PC'''. "Molecular Field Analysis (MFA) and other QSAR techniques in development of phosphatase inhibitors".<br />
''Anticancer Agents Med Chem.'' 2011 Jan;11(1):151-163. (Invited Review Article) <br><br />
<br />
4.'''Nair PC''', Sobhia ME. "Fingerprint directed scaffold hopping for identification of CCR2 antagonists".<br />
''J Chem Inf Model.'' 2008 Sep;48(9):1891-902. <br><br />
<br />
5.'''Nair PC''', Srikanth K, Sobhia ME. "QSAR studies on CCR2 antagonists with chiral sensitive hologram descriptors".<br />
''Bioorg Med Chem Lett.'' 2008 Feb 15;18(4):1323-30. <br><br />
<br />
6.Srikanth K, '''Nair PC''', Sobhia ME. "Probing the structural and topological requirements for CCR2 antagonism: holographic QSAR for <br> indolopiperidine derivatives".''Bioorg Med Chem Lett.'' 2008 Feb 15;18(4):1450-6. <br><br />
<br />
7.'''Nair PC''', Sobhia ME. "Comparative QSTR studies for predicting mutagenicity of nitro compounds".<br />
''J Mol Graph Model.'' 2008 Feb;26(6):916-34. <br><br />
<br />
8.'''Nair PC''', Sobhia ME. "Quantitative structure activity relationship studies on thiourea analogues as influenza virus neuraminidase inhibitors". ''Eur J Med Chem.'' 2008 Feb;43(2):293-9. <br><br />
<br />
9.'''Nair PC''', Sobhia ME."CoMFA based de novo design of pyridazine analogs as PTP1B inhibitors".<br />
''J Mol Graph Model.'' 2007 Jul;26(1):117-23. <br><br />
<br />
10.Khurana J, '''Nair P''',Sobhia ME. "Design of Allosteric Ligands Using Computer Aided Drug Design (CADD) Techniques", Current Research & Information on Pharmaceutical Sciences (CRIPS), 2006 Apr;7(2):8-13.(Review Article)<br><br />
<br />
== Poster Presentations ==<br />
1.'''Nair PC''', Malde AK, Mark AE."The structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-methyltransferase (PNMT): A Molecular Dynamics and Free Energy study", Molecular Modelling 2010, Melbourne, Australia, 28Nov-1Dec 2010.<br />
<br />
2.'''Nair PC''', Malde AK, Mark AE.Investigating structural requirements for PNMT inhibition: A molecular dynamics and free energy calculation study", Division of chemistry and structural biology symposium, Institute of Molecular Bioscience, Brisbane, Australia, Nov 18-19 2010.<br />
<br />
3.'''Nair PC''', Malde AK, Mark AE. "Investigation of ligand interaction and binding free Energy of 1,2,3,4 tetrahydroisoquinoline analogues as PNMT inhibitors", 61st Indian Pharmaceutical Congress, 11-13 December 2009.<br />
<br />
4.'''Nair PC''', Sobhia ME. "Identification of Novel CCR2 Scaffolds Through Fingerprint Directed Virtual Screening", Virtual Discovery Europe (Computer Aided Drug Design and Screening) London, England, 24-25 October 2007. (Presented by Dr. M. Elizabeth Sobhia, NIPER )<br />
<br />
5.'''Nair PC''', Sobhia ME. "Synergistic application of target structure based alignment and 3D-QSAR study of protein tyrosine phosphatases 1B (PTP1B) inhibitors", Workshop on Pharmcoinformatics: Tools for Drug Target Identification, NIPER, India, March 14-16, 2007.<br />
<br />
6.'''Nair PC''', Sobhia ME. "Quantitative Structure Toxicity Relationship (QSTR) Studies for Predicting Mutagenicity of Nitro Compounds", International Conference on Chemoinformatics, NCL, Pune, India, Jan 22, 2007.<br />
<br />
7.'''Nair PC''', Sobhia ME. "Design of novel PTP1B inhibitors using 3D-QSAR and concept of hypothetical cavity generation", Workshop on Pharmacoinformatics: QSAR, NIPER, India, March 3-4, 2006.<br />
<br />
== Other Conferences/Scientific visits ==<br />
<br />
Molecular Modelling (MM2009), Gold Coast, Queensland, Australia, July 26-29 2009. <br />
<br />
Attended 8th National Center of Competence in Research (NCCR) Practical Course in the area of computational structural biology, Kandersteg, Switzerland, Jan 10-15 2010.<br />
<br />
Visited as a scientific guest in the laboratory of Prof. Wilfred F. van Gunsteren, ETH Zurich, Switzerland, Jan 16-29 2010.<br />
<br />
== Contact Details ==<br />
<br />
Endeavour IPRS Doctoral Fellow <br><br />
Molecular Dynamics Group <br><br />
School of Chemistry and Molecular Biosciences (SCMB) <br><br />
Molecular Biosciences Building (#76) <br><br />
The University of Queensland <br><br />
St. Lucia Campus, Brisbane, QLD 4072 <br><br />
Australia <br><br />
<br />
'''email''' p.nair@uq.edu.au</div>PramodNairhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=File:Test.jpg&diff=15913File:Test.jpg2011-04-12T11:56:28Z<p>PramodNair: </p>
<hr />
<div></div>PramodNairhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Pramod_Nair&diff=15912Pramod Nair2011-04-12T11:55:58Z<p>PramodNair: /* Research Interests */</p>
<hr />
<div>Automated Force Field Topology Builder (ATB) for GROMOS and GROMACS : MD group of Prof. Alan E. Mark<br />
http://compbio.biosci.uq.edu.au/atb/ <br />
<br />
== Research Interests ==<br />
Computer Aided Drug Design (CADD) and Free Energy Calculations<br />
<br />
Alternate Free energy methods to aid high-throughput virtual screening in drug discovery<br />
<br />
Molecular Dynamics simulations of macromolecular and small molecular systems<br />
[[Image:test.jpg]]<br />
<br />
== Academic ==<br />
'''B. Pharm.''' Bombay College of Pharmacy, University of Mumbai, India 2001-2005 <br><br />
'''MS (Pharm.)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2005-2007 <br><br />
'''Junior Research Fellow (JRF)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2007-2008 <br><br />
'''PhD Student''' Molecular Dynamics Group, School of Chemistry and Molecular Biosciences (SCMB),University of Queensland, Australia 2009 <br><br />
<br />
== Publications ==<br />
1. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, '''Nair PC''', Oostenbrink C, Mark AE. An Automated force field Topology Builder (ATB) and repository: version 1.0. ''J Chem Theory Comput.'' 2011, submitted.<br />
<br />
2.'''Nair PC''', Malde AK, Mark AE."Using theory to reconcile experiment: the structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-MethylTransferase (PNMT)". ''J Chem Theory Comput.'' In press <br><br />
<br />
3.'''Nair PC'''. "Molecular Field Analysis (MFA) and other QSAR techniques in development of phosphatase inhibitors".<br />
''Anticancer Agents Med Chem.'' 2011 Jan;11(1):151-163. (Invited Review Article) <br><br />
<br />
4.'''Nair PC''', Sobhia ME. "Fingerprint directed scaffold hopping for identification of CCR2 antagonists".<br />
''J Chem Inf Model.'' 2008 Sep;48(9):1891-902. <br><br />
<br />
5.'''Nair PC''', Srikanth K, Sobhia ME. "QSAR studies on CCR2 antagonists with chiral sensitive hologram descriptors".<br />
''Bioorg Med Chem Lett.'' 2008 Feb 15;18(4):1323-30. <br><br />
<br />
6.Srikanth K, '''Nair PC''', Sobhia ME. "Probing the structural and topological requirements for CCR2 antagonism: holographic QSAR for <br> indolopiperidine derivatives".''Bioorg Med Chem Lett.'' 2008 Feb 15;18(4):1450-6. <br><br />
<br />
7.'''Nair PC''', Sobhia ME. "Comparative QSTR studies for predicting mutagenicity of nitro compounds".<br />
''J Mol Graph Model.'' 2008 Feb;26(6):916-34. <br><br />
<br />
8.'''Nair PC''', Sobhia ME. "Quantitative structure activity relationship studies on thiourea analogues as influenza virus neuraminidase inhibitors". ''Eur J Med Chem.'' 2008 Feb;43(2):293-9. <br><br />
<br />
9.'''Nair PC''', Sobhia ME."CoMFA based de novo design of pyridazine analogs as PTP1B inhibitors".<br />
''J Mol Graph Model.'' 2007 Jul;26(1):117-23. <br><br />
<br />
10.Khurana J, '''Nair P''',Sobhia ME. "Design of Allosteric Ligands Using Computer Aided Drug Design (CADD) Techniques", Current Research & Information on Pharmaceutical Sciences (CRIPS), 2006 Apr;7(2):8-13.(Review Article)<br><br />
<br />
== Poster Presentations ==<br />
1.'''Nair PC''', Malde AK, Mark AE."The structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-methyltransferase (PNMT): A Molecular Dynamics and Free Energy study", Molecular Modelling 2010, Melbourne, Australia, 28Nov-1Dec 2010.<br />
<br />
2.'''Nair PC''', Malde AK, Mark AE.Investigating structural requirements for PNMT inhibition: A molecular dynamics and free energy calculation study", Division of chemistry and structural biology symposium, Institute of Molecular Bioscience, Brisbane, Australia, Nov 18-19 2010.<br />
<br />
3.'''Nair PC''', Malde AK, Mark AE. "Investigation of ligand interaction and binding free Energy of 1,2,3,4 tetrahydroisoquinoline analogues as PNMT inhibitors", 61st Indian Pharmaceutical Congress, 11-13 December 2009.<br />
<br />
4.'''Nair PC''', Sobhia ME. "Identification of Novel CCR2 Scaffolds Through Fingerprint Directed Virtual Screening", Virtual Discovery Europe (Computer Aided Drug Design and Screening) London, England, 24-25 October 2007. (Presented by Dr. M. Elizabeth Sobhia, NIPER )<br />
<br />
5.'''Nair PC''', Sobhia ME. "Synergistic application of target structure based alignment and 3D-QSAR study of protein tyrosine phosphatases 1B (PTP1B) inhibitors", Workshop on Pharmcoinformatics: Tools for Drug Target Identification, NIPER, India, March 14-16, 2007.<br />
<br />
6.'''Nair PC''', Sobhia ME. "Quantitative Structure Toxicity Relationship (QSTR) Studies for Predicting Mutagenicity of Nitro Compounds", International Conference on Chemoinformatics, NCL, Pune, India, Jan 22, 2007.<br />
<br />
7.'''Nair PC''', Sobhia ME. "Design of novel PTP1B inhibitors using 3D-QSAR and concept of hypothetical cavity generation", Workshop on Pharmacoinformatics: QSAR, NIPER, India, March 3-4, 2006.<br />
<br />
== Other Conferences/Scientific visits ==<br />
<br />
Molecular Modelling (MM2009), Gold Coast, Queensland, Australia, July 26-29 2009. <br />
<br />
Attended 8th National Center of Competence in Research (NCCR) Practical Course in the area of computational structural biology, Kandersteg, Switzerland, Jan 10-15 2010.<br />
<br />
Visited as a scientific guest in the laboratory of Prof. Wilfred F. van Gunsteren, ETH Zurich, Switzerland, Jan 16-29 2010.<br />
<br />
== Contact Details ==<br />
<br />
Endeavour IPRS Doctoral Fellow <br><br />
Molecular Dynamics Group <br><br />
School of Chemistry and Molecular Biosciences (SCMB) <br><br />
Molecular Biosciences Building (#76) <br><br />
The University of Queensland <br><br />
St. Lucia Campus, Brisbane, QLD 4072 <br><br />
Australia <br><br />
<br />
'''email''' p.nair@uq.edu.au</div>PramodNairhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Pramod_Nair&diff=15909Pramod Nair2011-04-11T09:00:19Z<p>PramodNair: /* Publications */</p>
<hr />
<div>Automated Force Field Topology Builder (ATB) for GROMOS and GROMACS : MD group of Prof. Alan E. Mark<br />
http://compbio.biosci.uq.edu.au/atb/ <br />
<br />
== Research Interests ==<br />
Computer Aided Drug Design (CADD) and Free Energy Calculations<br />
<br />
Alternate Free energy methods to aid high-throughput virtual screening in drug discovery<br />
<br />
Molecular Dynamics simulations of macromolecular and small molecular systems<br />
<br />
== Academic ==<br />
'''B. Pharm.''' Bombay College of Pharmacy, University of Mumbai, India 2001-2005 <br><br />
'''MS (Pharm.)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2005-2007 <br><br />
'''Junior Research Fellow (JRF)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2007-2008 <br><br />
'''PhD Student''' Molecular Dynamics Group, School of Chemistry and Molecular Biosciences (SCMB),University of Queensland, Australia 2009 <br><br />
<br />
== Publications ==<br />
1. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, '''Nair PC''', Oostenbrink C, Mark AE. An Automated force field Topology Builder (ATB) and repository: version 1.0. ''J Chem Theory Comput.'' 2011, submitted.<br />
<br />
2.'''Nair PC''', Malde AK, Mark AE."Using theory to reconcile experiment: the structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-MethylTransferase (PNMT)". ''J Chem Theory Comput.'' In press <br><br />
<br />
3.'''Nair PC'''. "Molecular Field Analysis (MFA) and other QSAR techniques in development of phosphatase inhibitors".<br />
''Anticancer Agents Med Chem.'' 2011 Jan;11(1):151-163. (Invited Review Article) <br><br />
<br />
4.'''Nair PC''', Sobhia ME. "Fingerprint directed scaffold hopping for identification of CCR2 antagonists".<br />
''J Chem Inf Model.'' 2008 Sep;48(9):1891-902. <br><br />
<br />
5.'''Nair PC''', Srikanth K, Sobhia ME. "QSAR studies on CCR2 antagonists with chiral sensitive hologram descriptors".<br />
''Bioorg Med Chem Lett.'' 2008 Feb 15;18(4):1323-30. <br><br />
<br />
6.Srikanth K, '''Nair PC''', Sobhia ME. "Probing the structural and topological requirements for CCR2 antagonism: holographic QSAR for <br> indolopiperidine derivatives".''Bioorg Med Chem Lett.'' 2008 Feb 15;18(4):1450-6. <br><br />
<br />
7.'''Nair PC''', Sobhia ME. "Comparative QSTR studies for predicting mutagenicity of nitro compounds".<br />
''J Mol Graph Model.'' 2008 Feb;26(6):916-34. <br><br />
<br />
8.'''Nair PC''', Sobhia ME. "Quantitative structure activity relationship studies on thiourea analogues as influenza virus neuraminidase inhibitors". ''Eur J Med Chem.'' 2008 Feb;43(2):293-9. <br><br />
<br />
9.'''Nair PC''', Sobhia ME."CoMFA based de novo design of pyridazine analogs as PTP1B inhibitors".<br />
''J Mol Graph Model.'' 2007 Jul;26(1):117-23. <br><br />
<br />
10.Khurana J, '''Nair P''',Sobhia ME. "Design of Allosteric Ligands Using Computer Aided Drug Design (CADD) Techniques", Current Research & Information on Pharmaceutical Sciences (CRIPS), 2006 Apr;7(2):8-13.(Review Article)<br><br />
<br />
== Poster Presentations ==<br />
1.'''Nair PC''', Malde AK, Mark AE."The structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-methyltransferase (PNMT): A Molecular Dynamics and Free Energy study", Molecular Modelling 2010, Melbourne, Australia, 28Nov-1Dec 2010.<br />
<br />
2.'''Nair PC''', Malde AK, Mark AE.Investigating structural requirements for PNMT inhibition: A molecular dynamics and free energy calculation study", Division of chemistry and structural biology symposium, Institute of Molecular Bioscience, Brisbane, Australia, Nov 18-19 2010.<br />
<br />
3.'''Nair PC''', Malde AK, Mark AE. "Investigation of ligand interaction and binding free Energy of 1,2,3,4 tetrahydroisoquinoline analogues as PNMT inhibitors", 61st Indian Pharmaceutical Congress, 11-13 December 2009.<br />
<br />
4.'''Nair PC''', Sobhia ME. "Identification of Novel CCR2 Scaffolds Through Fingerprint Directed Virtual Screening", Virtual Discovery Europe (Computer Aided Drug Design and Screening) London, England, 24-25 October 2007. (Presented by Dr. M. Elizabeth Sobhia, NIPER )<br />
<br />
5.'''Nair PC''', Sobhia ME. "Synergistic application of target structure based alignment and 3D-QSAR study of protein tyrosine phosphatases 1B (PTP1B) inhibitors", Workshop on Pharmcoinformatics: Tools for Drug Target Identification, NIPER, India, March 14-16, 2007.<br />
<br />
6.'''Nair PC''', Sobhia ME. "Quantitative Structure Toxicity Relationship (QSTR) Studies for Predicting Mutagenicity of Nitro Compounds", International Conference on Chemoinformatics, NCL, Pune, India, Jan 22, 2007.<br />
<br />
7.'''Nair PC''', Sobhia ME. "Design of novel PTP1B inhibitors using 3D-QSAR and concept of hypothetical cavity generation", Workshop on Pharmacoinformatics: QSAR, NIPER, India, March 3-4, 2006.<br />
<br />
== Other Conferences/Scientific visits ==<br />
<br />
Molecular Modelling (MM2009), Gold Coast, Queensland, Australia, July 26-29 2009. <br />
<br />
Attended 8th National Center of Competence in Research (NCCR) Practical Course in the area of computational structural biology, Kandersteg, Switzerland, Jan 10-15 2010.<br />
<br />
Visited as a scientific guest in the laboratory of Prof. Wilfred F. van Gunsteren, ETH Zurich, Switzerland, Jan 16-29 2010.<br />
<br />
== Contact Details ==<br />
<br />
Endeavour IPRS Doctoral Fellow <br><br />
Molecular Dynamics Group <br><br />
School of Chemistry and Molecular Biosciences (SCMB) <br><br />
Molecular Biosciences Building (#76) <br><br />
The University of Queensland <br><br />
St. Lucia Campus, Brisbane, QLD 4072 <br><br />
Australia <br><br />
<br />
'''email''' p.nair@uq.edu.au</div>PramodNairhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Pramod_Nair&diff=15908Pramod Nair2011-04-11T08:59:48Z<p>PramodNair: /* Publications */</p>
<hr />
<div>Automated Force Field Topology Builder (ATB) for GROMOS and GROMACS : MD group of Prof. Alan E. Mark<br />
http://compbio.biosci.uq.edu.au/atb/ <br />
<br />
== Research Interests ==<br />
Computer Aided Drug Design (CADD) and Free Energy Calculations<br />
<br />
Alternate Free energy methods to aid high-throughput virtual screening in drug discovery<br />
<br />
Molecular Dynamics simulations of macromolecular and small molecular systems<br />
<br />
== Academic ==<br />
'''B. Pharm.''' Bombay College of Pharmacy, University of Mumbai, India 2001-2005 <br><br />
'''MS (Pharm.)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2005-2007 <br><br />
'''Junior Research Fellow (JRF)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2007-2008 <br><br />
'''PhD Student''' Molecular Dynamics Group, School of Chemistry and Molecular Biosciences (SCMB),University of Queensland, Australia 2009 <br><br />
<br />
== Publications ==<br />
1. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, '''Nair PC''', Oostenbrink C, Mark AE. An Automated force field Topology Builder (ATB) and repository: version 1.0. ''J Chem Theory Comput.'' 2011, submitted.<br />
<br />
2.'''Nair PC''', Malde AK, Mark AE."Using theory to reconcile experiment: the structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-MethylTransferase (PNMT)". ''J Chem Theory Comput.'' In press <br><br />
<br />
3.'''Nair PC'''. "Molecular Field Analysis (MFA) and other QSAR techniques in development of phosphatase inhibitors".<br />
''Anticancer Agents Med Chem.'' 2011 Jan;11(1):151-163. (Invited Review) <br><br />
<br />
4.'''Nair PC''', Sobhia ME. "Fingerprint directed scaffold hopping for identification of CCR2 antagonists".<br />
''J Chem Inf Model.'' 2008 Sep;48(9):1891-902. <br><br />
<br />
5.'''Nair PC''', Srikanth K, Sobhia ME. "QSAR studies on CCR2 antagonists with chiral sensitive hologram descriptors".<br />
''Bioorg Med Chem Lett.'' 2008 Feb 15;18(4):1323-30. <br><br />
<br />
6.Srikanth K, '''Nair PC''', Sobhia ME. "Probing the structural and topological requirements for CCR2 antagonism: holographic QSAR for <br> indolopiperidine derivatives".''Bioorg Med Chem Lett.'' 2008 Feb 15;18(4):1450-6. <br><br />
<br />
7.'''Nair PC''', Sobhia ME. "Comparative QSTR studies for predicting mutagenicity of nitro compounds".<br />
''J Mol Graph Model.'' 2008 Feb;26(6):916-34. <br><br />
<br />
8.'''Nair PC''', Sobhia ME. "Quantitative structure activity relationship studies on thiourea analogues as influenza virus neuraminidase inhibitors". ''Eur J Med Chem.'' 2008 Feb;43(2):293-9. <br><br />
<br />
9.'''Nair PC''', Sobhia ME."CoMFA based de novo design of pyridazine analogs as PTP1B inhibitors".<br />
''J Mol Graph Model.'' 2007 Jul;26(1):117-23. <br><br />
<br />
10.Khurana J, '''Nair P''',Sobhia ME. "Design of Allosteric Ligands Using Computer Aided Drug Design (CADD) Techniques", Current Research & Information on Pharmaceutical Sciences (CRIPS), 2006 Apr;7(2):8-13.(Review Article)<br><br />
<br />
== Poster Presentations ==<br />
1.'''Nair PC''', Malde AK, Mark AE."The structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-methyltransferase (PNMT): A Molecular Dynamics and Free Energy study", Molecular Modelling 2010, Melbourne, Australia, 28Nov-1Dec 2010.<br />
<br />
2.'''Nair PC''', Malde AK, Mark AE.Investigating structural requirements for PNMT inhibition: A molecular dynamics and free energy calculation study", Division of chemistry and structural biology symposium, Institute of Molecular Bioscience, Brisbane, Australia, Nov 18-19 2010.<br />
<br />
3.'''Nair PC''', Malde AK, Mark AE. "Investigation of ligand interaction and binding free Energy of 1,2,3,4 tetrahydroisoquinoline analogues as PNMT inhibitors", 61st Indian Pharmaceutical Congress, 11-13 December 2009.<br />
<br />
4.'''Nair PC''', Sobhia ME. "Identification of Novel CCR2 Scaffolds Through Fingerprint Directed Virtual Screening", Virtual Discovery Europe (Computer Aided Drug Design and Screening) London, England, 24-25 October 2007. (Presented by Dr. M. Elizabeth Sobhia, NIPER )<br />
<br />
5.'''Nair PC''', Sobhia ME. "Synergistic application of target structure based alignment and 3D-QSAR study of protein tyrosine phosphatases 1B (PTP1B) inhibitors", Workshop on Pharmcoinformatics: Tools for Drug Target Identification, NIPER, India, March 14-16, 2007.<br />
<br />
6.'''Nair PC''', Sobhia ME. "Quantitative Structure Toxicity Relationship (QSTR) Studies for Predicting Mutagenicity of Nitro Compounds", International Conference on Chemoinformatics, NCL, Pune, India, Jan 22, 2007.<br />
<br />
7.'''Nair PC''', Sobhia ME. "Design of novel PTP1B inhibitors using 3D-QSAR and concept of hypothetical cavity generation", Workshop on Pharmacoinformatics: QSAR, NIPER, India, March 3-4, 2006.<br />
<br />
== Other Conferences/Scientific visits ==<br />
<br />
Molecular Modelling (MM2009), Gold Coast, Queensland, Australia, July 26-29 2009. <br />
<br />
Attended 8th National Center of Competence in Research (NCCR) Practical Course in the area of computational structural biology, Kandersteg, Switzerland, Jan 10-15 2010.<br />
<br />
Visited as a scientific guest in the laboratory of Prof. Wilfred F. van Gunsteren, ETH Zurich, Switzerland, Jan 16-29 2010.<br />
<br />
== Contact Details ==<br />
<br />
Endeavour IPRS Doctoral Fellow <br><br />
Molecular Dynamics Group <br><br />
School of Chemistry and Molecular Biosciences (SCMB) <br><br />
Molecular Biosciences Building (#76) <br><br />
The University of Queensland <br><br />
St. Lucia Campus, Brisbane, QLD 4072 <br><br />
Australia <br><br />
<br />
'''email''' p.nair@uq.edu.au</div>PramodNairhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Pramod_Nair&diff=15907Pramod Nair2011-04-11T08:58:55Z<p>PramodNair: /* Publications */</p>
<hr />
<div>Automated Force Field Topology Builder (ATB) for GROMOS and GROMACS : MD group of Prof. Alan E. Mark<br />
http://compbio.biosci.uq.edu.au/atb/ <br />
<br />
== Research Interests ==<br />
Computer Aided Drug Design (CADD) and Free Energy Calculations<br />
<br />
Alternate Free energy methods to aid high-throughput virtual screening in drug discovery<br />
<br />
Molecular Dynamics simulations of macromolecular and small molecular systems<br />
<br />
== Academic ==<br />
'''B. Pharm.''' Bombay College of Pharmacy, University of Mumbai, India 2001-2005 <br><br />
'''MS (Pharm.)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2005-2007 <br><br />
'''Junior Research Fellow (JRF)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2007-2008 <br><br />
'''PhD Student''' Molecular Dynamics Group, School of Chemistry and Molecular Biosciences (SCMB),University of Queensland, Australia 2009 <br><br />
<br />
== Publications ==<br />
1. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, '''Nair PC''', Oostenbrink C, Mark AE. An Automated force field Topology Builder (ATB) and repository: version 1.0. ''J Chem Theory Comput.'' 2011, submitted.<br />
<br />
2.'''Nair PC''', Malde AK, Mark AE."Using theory to reconcile experiment: the structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-MethylTransferase (PNMT)". ''J Chem Theory Comput.'' In press <br><br />
<br />
3.'''Nair PC'''. "Molecular Field Analysis (MFA) and other QSAR techniques in development of phosphatase inhibitors".<br />
''Anticancer Agents Med Chem.'' 2011 Jan;11(1):151-163. <br><br />
<br />
4.'''Nair PC''', Sobhia ME. "Fingerprint directed scaffold hopping for identification of CCR2 antagonists".<br />
''J Chem Inf Model.'' 2008 Sep;48(9):1891-902. <br><br />
<br />
5.'''Nair PC''', Srikanth K, Sobhia ME. "QSAR studies on CCR2 antagonists with chiral sensitive hologram descriptors".<br />
''Bioorg Med Chem Lett.'' 2008 Feb 15;18(4):1323-30. <br><br />
<br />
6.Srikanth K, '''Nair PC''', Sobhia ME. "Probing the structural and topological requirements for CCR2 antagonism: holographic QSAR for <br> indolopiperidine derivatives".''Bioorg Med Chem Lett.'' 2008 Feb 15;18(4):1450-6. <br><br />
<br />
7.'''Nair PC''', Sobhia ME. "Comparative QSTR studies for predicting mutagenicity of nitro compounds".<br />
''J Mol Graph Model.'' 2008 Feb;26(6):916-34. <br><br />
<br />
8.'''Nair PC''', Sobhia ME. "Quantitative structure activity relationship studies on thiourea analogues as influenza virus neuraminidase inhibitors". ''Eur J Med Chem.'' 2008 Feb;43(2):293-9. <br><br />
<br />
9.'''Nair PC''', Sobhia ME."CoMFA based de novo design of pyridazine analogs as PTP1B inhibitors".<br />
''J Mol Graph Model.'' 2007 Jul;26(1):117-23. <br><br />
<br />
10.Khurana J, '''Nair P''',Sobhia ME. "Design of Allosteric Ligands Using Computer Aided Drug Design (CADD) Techniques", Current Research & Information on Pharmaceutical Sciences (CRIPS), 2006 Apr;7(2):8-13. <br> (Review Article)<br />
<br />
== Poster Presentations ==<br />
1.'''Nair PC''', Malde AK, Mark AE."The structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-methyltransferase (PNMT): A Molecular Dynamics and Free Energy study", Molecular Modelling 2010, Melbourne, Australia, 28Nov-1Dec 2010.<br />
<br />
2.'''Nair PC''', Malde AK, Mark AE.Investigating structural requirements for PNMT inhibition: A molecular dynamics and free energy calculation study", Division of chemistry and structural biology symposium, Institute of Molecular Bioscience, Brisbane, Australia, Nov 18-19 2010.<br />
<br />
3.'''Nair PC''', Malde AK, Mark AE. "Investigation of ligand interaction and binding free Energy of 1,2,3,4 tetrahydroisoquinoline analogues as PNMT inhibitors", 61st Indian Pharmaceutical Congress, 11-13 December 2009.<br />
<br />
4.'''Nair PC''', Sobhia ME. "Identification of Novel CCR2 Scaffolds Through Fingerprint Directed Virtual Screening", Virtual Discovery Europe (Computer Aided Drug Design and Screening) London, England, 24-25 October 2007. (Presented by Dr. M. Elizabeth Sobhia, NIPER )<br />
<br />
5.'''Nair PC''', Sobhia ME. "Synergistic application of target structure based alignment and 3D-QSAR study of protein tyrosine phosphatases 1B (PTP1B) inhibitors", Workshop on Pharmcoinformatics: Tools for Drug Target Identification, NIPER, India, March 14-16, 2007.<br />
<br />
6.'''Nair PC''', Sobhia ME. "Quantitative Structure Toxicity Relationship (QSTR) Studies for Predicting Mutagenicity of Nitro Compounds", International Conference on Chemoinformatics, NCL, Pune, India, Jan 22, 2007.<br />
<br />
7.'''Nair PC''', Sobhia ME. "Design of novel PTP1B inhibitors using 3D-QSAR and concept of hypothetical cavity generation", Workshop on Pharmacoinformatics: QSAR, NIPER, India, March 3-4, 2006.<br />
<br />
== Other Conferences/Scientific visits ==<br />
<br />
Molecular Modelling (MM2009), Gold Coast, Queensland, Australia, July 26-29 2009. <br />
<br />
Attended 8th National Center of Competence in Research (NCCR) Practical Course in the area of computational structural biology, Kandersteg, Switzerland, Jan 10-15 2010.<br />
<br />
Visited as a scientific guest in the laboratory of Prof. Wilfred F. van Gunsteren, ETH Zurich, Switzerland, Jan 16-29 2010.<br />
<br />
== Contact Details ==<br />
<br />
Endeavour IPRS Doctoral Fellow <br><br />
Molecular Dynamics Group <br><br />
School of Chemistry and Molecular Biosciences (SCMB) <br><br />
Molecular Biosciences Building (#76) <br><br />
The University of Queensland <br><br />
St. Lucia Campus, Brisbane, QLD 4072 <br><br />
Australia <br><br />
<br />
'''email''' p.nair@uq.edu.au</div>PramodNairhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Pramod_Nair&diff=15906Pramod Nair2011-04-11T08:57:51Z<p>PramodNair: /* Publications */</p>
<hr />
<div>Automated Force Field Topology Builder (ATB) for GROMOS and GROMACS : MD group of Prof. Alan E. Mark<br />
http://compbio.biosci.uq.edu.au/atb/ <br />
<br />
== Research Interests ==<br />
Computer Aided Drug Design (CADD) and Free Energy Calculations<br />
<br />
Alternate Free energy methods to aid high-throughput virtual screening in drug discovery<br />
<br />
Molecular Dynamics simulations of macromolecular and small molecular systems<br />
<br />
== Academic ==<br />
'''B. Pharm.''' Bombay College of Pharmacy, University of Mumbai, India 2001-2005 <br><br />
'''MS (Pharm.)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2005-2007 <br><br />
'''Junior Research Fellow (JRF)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2007-2008 <br><br />
'''PhD Student''' Molecular Dynamics Group, School of Chemistry and Molecular Biosciences (SCMB),University of Queensland, Australia 2009 <br><br />
<br />
== Publications ==<br />
1. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, '''Nair PC''', Oostenbrink C, Mark AE. An Automated force field Topology Builder (ATB) and repository: version 1.0. ''J Chem Theory Comput.'' 2011, submitted.<br />
<br />
2.'''Nair PC''', Malde AK, Mark AE."Using theory to reconcile experiment: the structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-MethylTransferase (PNMT)". ''J Chem Theory Comput.'' In press <br><br />
<br />
3.'''Nair PC'''. "Molecular Field Analysis (MFA) and other QSAR techniques in development of phosphatase inhibitors".<br />
''Anticancer Agents Med Chem.'' 2011 Jan;11(1):151-163. <br><br />
<br />
4.'''Nair PC''', Sobhia ME. "Fingerprint directed scaffold hopping for identification of CCR2 antagonists".<br />
''J Chem Inf Model.'' 2008 Sep;48(9):1891-902. <br><br />
<br />
5.'''Nair PC''', Srikanth K, Sobhia ME. "QSAR studies on CCR2 antagonists with chiral sensitive hologram descriptors".<br />
''Bioorg Med Chem Lett.'' 2008 Feb 15;18(4):1323-30. <br><br />
<br />
6.Srikanth K, '''Nair PC''', Sobhia ME. "Probing the structural and topological requirements for CCR2 antagonism: holographic QSAR for <br> indolopiperidine derivatives".''Bioorg Med Chem Lett.'' 2008 Feb 15;18(4):1450-6. <br><br />
<br />
7.'''Nair PC''', Sobhia ME. "Comparative QSTR studies for predicting mutagenicity of nitro compounds".<br />
''J Mol Graph Model.'' 2008 Feb;26(6):916-34. <br><br />
<br />
8.'''Nair PC''', Sobhia ME. "Quantitative structure activity relationship studies on thiourea analogues as influenza virus neuraminidase inhibitors". ''Eur J Med Chem.'' 2008 Feb;43(2):293-9. <br><br />
<br />
9.'''Nair PC''', Sobhia ME."CoMFA based de novo design of pyridazine analogs as PTP1B inhibitors".<br />
''J Mol Graph Model.'' 2007 Jul;26(1):117-23. <br><br />
<br />
10.Khurana J, '''Nair P''',Sobhia ME. Design of Allosteric Ligands Using Computer Aided Drug Design (CADD) Techniques (Review Article), Current Research & Information on Pharmaceutical Sciences (CRIPS), 2006 Apr;7(2):8-13. <br><br />
<br />
== Poster Presentations ==<br />
1.'''Nair PC''', Malde AK, Mark AE."The structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-methyltransferase (PNMT): A Molecular Dynamics and Free Energy study", Molecular Modelling 2010, Melbourne, Australia, 28Nov-1Dec 2010.<br />
<br />
2.'''Nair PC''', Malde AK, Mark AE.Investigating structural requirements for PNMT inhibition: A molecular dynamics and free energy calculation study", Division of chemistry and structural biology symposium, Institute of Molecular Bioscience, Brisbane, Australia, Nov 18-19 2010.<br />
<br />
3.'''Nair PC''', Malde AK, Mark AE. "Investigation of ligand interaction and binding free Energy of 1,2,3,4 tetrahydroisoquinoline analogues as PNMT inhibitors", 61st Indian Pharmaceutical Congress, 11-13 December 2009.<br />
<br />
4.'''Nair PC''', Sobhia ME. "Identification of Novel CCR2 Scaffolds Through Fingerprint Directed Virtual Screening", Virtual Discovery Europe (Computer Aided Drug Design and Screening) London, England, 24-25 October 2007. (Presented by Dr. M. Elizabeth Sobhia, NIPER )<br />
<br />
5.'''Nair PC''', Sobhia ME. "Synergistic application of target structure based alignment and 3D-QSAR study of protein tyrosine phosphatases 1B (PTP1B) inhibitors", Workshop on Pharmcoinformatics: Tools for Drug Target Identification, NIPER, India, March 14-16, 2007.<br />
<br />
6.'''Nair PC''', Sobhia ME. "Quantitative Structure Toxicity Relationship (QSTR) Studies for Predicting Mutagenicity of Nitro Compounds", International Conference on Chemoinformatics, NCL, Pune, India, Jan 22, 2007.<br />
<br />
7.'''Nair PC''', Sobhia ME. "Design of novel PTP1B inhibitors using 3D-QSAR and concept of hypothetical cavity generation", Workshop on Pharmacoinformatics: QSAR, NIPER, India, March 3-4, 2006.<br />
<br />
== Other Conferences/Scientific visits ==<br />
<br />
Molecular Modelling (MM2009), Gold Coast, Queensland, Australia, July 26-29 2009. <br />
<br />
Attended 8th National Center of Competence in Research (NCCR) Practical Course in the area of computational structural biology, Kandersteg, Switzerland, Jan 10-15 2010.<br />
<br />
Visited as a scientific guest in the laboratory of Prof. Wilfred F. van Gunsteren, ETH Zurich, Switzerland, Jan 16-29 2010.<br />
<br />
== Contact Details ==<br />
<br />
Endeavour IPRS Doctoral Fellow <br><br />
Molecular Dynamics Group <br><br />
School of Chemistry and Molecular Biosciences (SCMB) <br><br />
Molecular Biosciences Building (#76) <br><br />
The University of Queensland <br><br />
St. Lucia Campus, Brisbane, QLD 4072 <br><br />
Australia <br><br />
<br />
'''email''' p.nair@uq.edu.au</div>PramodNairhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Pramod_Nair&diff=15905Pramod Nair2011-04-11T08:57:16Z<p>PramodNair: /* Publications */</p>
<hr />
<div>Automated Force Field Topology Builder (ATB) for GROMOS and GROMACS : MD group of Prof. Alan E. Mark<br />
http://compbio.biosci.uq.edu.au/atb/ <br />
<br />
== Research Interests ==<br />
Computer Aided Drug Design (CADD) and Free Energy Calculations<br />
<br />
Alternate Free energy methods to aid high-throughput virtual screening in drug discovery<br />
<br />
Molecular Dynamics simulations of macromolecular and small molecular systems<br />
<br />
== Academic ==<br />
'''B. Pharm.''' Bombay College of Pharmacy, University of Mumbai, India 2001-2005 <br><br />
'''MS (Pharm.)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2005-2007 <br><br />
'''Junior Research Fellow (JRF)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2007-2008 <br><br />
'''PhD Student''' Molecular Dynamics Group, School of Chemistry and Molecular Biosciences (SCMB),University of Queensland, Australia 2009 <br><br />
<br />
== Publications ==<br />
1. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, '''Nair PC''', Oostenbrink C, Mark AE. An Automated force field Topology Builder (ATB) and repository: version 1.0. ''J Chem Theory Comput.'' 2011, submitted.<br />
<br />
2.'''Nair PC''', Malde AK, Mark AE."Using theory to reconcile experiment: the structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-MethylTransferase (PNMT)". ''J Chem Theory Comput.'' In press <br><br />
<br />
3.'''Nair PC'''. "Molecular Field Analysis (MFA) and other QSAR techniques in development of phosphatase inhibitors".<br />
''Anticancer Agents Med Chem.'' 2011 Jan;11(1):151-163. <br><br />
<br />
4.'''Nair PC''', Sobhia ME. "Fingerprint directed scaffold hopping for identification of CCR2 antagonists".<br />
''J Chem Inf Model.'' 2008 Sep;48(9):1891-902. <br><br />
<br />
5.'''Nair PC''', Srikanth K, Sobhia ME. "QSAR studies on CCR2 antagonists with chiral sensitive hologram descriptors".<br />
''Bioorg Med Chem Lett.'' 2008 Feb 15;18(4):1323-30. <br><br />
<br />
6.Srikanth K, '''Nair PC''', Sobhia ME. "Probing the structural and topological requirements for CCR2 antagonism: holographic QSAR for <br> indolopiperidine derivatives".''Bioorg Med Chem Lett.'' 2008 Feb 15;18(4):1450-6. <br><br />
<br />
7.'''Nair PC''', Sobhia ME. "Comparative QSTR studies for predicting mutagenicity of nitro compounds".<br />
''J Mol Graph Model.'' 2008 Feb;26(6):916-34. <br><br />
<br />
8.'''Nair PC''', Sobhia ME. "Quantitative structure activity relationship studies on thiourea analogues as influenza virus neuraminidase inhibitors". ''Eur J Med Chem.'' 2008 Feb;43(2):293-9. <br><br />
<br />
9.'''Nair PC''', Sobhia ME."CoMFA based de novo design of pyridazine analogs as PTP1B inhibitors".<br />
''J Mol Graph Model.'' 2007 Jul;26(1):117-23. <br><br />
<br />
10.Khurana J,'''Nair P''',Sobhia ME. Design of Allosteric Ligands Using Computer Aided Drug Design (CADD) Techniques (Review Article), Current Research & Information on Pharmaceutical Sciences (CRIPS), 2006 Apr;7(2):8-13. <br><br />
<br />
== Poster Presentations ==<br />
1.'''Nair PC''', Malde AK, Mark AE."The structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-methyltransferase (PNMT): A Molecular Dynamics and Free Energy study", Molecular Modelling 2010, Melbourne, Australia, 28Nov-1Dec 2010.<br />
<br />
2.'''Nair PC''', Malde AK, Mark AE.Investigating structural requirements for PNMT inhibition: A molecular dynamics and free energy calculation study", Division of chemistry and structural biology symposium, Institute of Molecular Bioscience, Brisbane, Australia, Nov 18-19 2010.<br />
<br />
3.'''Nair PC''', Malde AK, Mark AE. "Investigation of ligand interaction and binding free Energy of 1,2,3,4 tetrahydroisoquinoline analogues as PNMT inhibitors", 61st Indian Pharmaceutical Congress, 11-13 December 2009.<br />
<br />
4.'''Nair PC''', Sobhia ME. "Identification of Novel CCR2 Scaffolds Through Fingerprint Directed Virtual Screening", Virtual Discovery Europe (Computer Aided Drug Design and Screening) London, England, 24-25 October 2007. (Presented by Dr. M. Elizabeth Sobhia, NIPER )<br />
<br />
5.'''Nair PC''', Sobhia ME. "Synergistic application of target structure based alignment and 3D-QSAR study of protein tyrosine phosphatases 1B (PTP1B) inhibitors", Workshop on Pharmcoinformatics: Tools for Drug Target Identification, NIPER, India, March 14-16, 2007.<br />
<br />
6.'''Nair PC''', Sobhia ME. "Quantitative Structure Toxicity Relationship (QSTR) Studies for Predicting Mutagenicity of Nitro Compounds", International Conference on Chemoinformatics, NCL, Pune, India, Jan 22, 2007.<br />
<br />
7.'''Nair PC''', Sobhia ME. "Design of novel PTP1B inhibitors using 3D-QSAR and concept of hypothetical cavity generation", Workshop on Pharmacoinformatics: QSAR, NIPER, India, March 3-4, 2006.<br />
<br />
== Other Conferences/Scientific visits ==<br />
<br />
Molecular Modelling (MM2009), Gold Coast, Queensland, Australia, July 26-29 2009. <br />
<br />
Attended 8th National Center of Competence in Research (NCCR) Practical Course in the area of computational structural biology, Kandersteg, Switzerland, Jan 10-15 2010.<br />
<br />
Visited as a scientific guest in the laboratory of Prof. Wilfred F. van Gunsteren, ETH Zurich, Switzerland, Jan 16-29 2010.<br />
<br />
== Contact Details ==<br />
<br />
Endeavour IPRS Doctoral Fellow <br><br />
Molecular Dynamics Group <br><br />
School of Chemistry and Molecular Biosciences (SCMB) <br><br />
Molecular Biosciences Building (#76) <br><br />
The University of Queensland <br><br />
St. Lucia Campus, Brisbane, QLD 4072 <br><br />
Australia <br><br />
<br />
'''email''' p.nair@uq.edu.au</div>PramodNairhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Pramod_Nair&diff=15904Pramod Nair2011-04-01T12:28:29Z<p>PramodNair: /* Publications */</p>
<hr />
<div>Automated Force Field Topology Builder (ATB) for GROMOS and GROMACS : MD group of Prof. Alan E. Mark<br />
http://compbio.biosci.uq.edu.au/atb/ <br />
<br />
== Research Interests ==<br />
Computer Aided Drug Design (CADD) and Free Energy Calculations<br />
<br />
Alternate Free energy methods to aid high-throughput virtual screening in drug discovery<br />
<br />
Molecular Dynamics simulations of macromolecular and small molecular systems<br />
<br />
== Academic ==<br />
'''B. Pharm.''' Bombay College of Pharmacy, University of Mumbai, India 2001-2005 <br><br />
'''MS (Pharm.)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2005-2007 <br><br />
'''Junior Research Fellow (JRF)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2007-2008 <br><br />
'''PhD Student''' Molecular Dynamics Group, School of Chemistry and Molecular Biosciences (SCMB),University of Queensland, Australia 2009 <br><br />
<br />
== Publications ==<br />
1. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, '''Nair PC''', Oostenbrink C, Mark AE. An Automated force field Topology Builder (ATB) and repository: version 1.0. ''J Chem Theory Comput.'' 2011, submitted.<br />
<br />
2.'''Nair PC''', Malde AK, Mark AE."Using theory to reconcile experiment: the structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-MethylTransferase (PNMT)". ''J Chem Theory Comput.'' In press <br><br />
<br />
3.'''Nair PC'''. "Molecular Field Analysis (MFA) and other QSAR techniques in development of phosphatase inhibitors".<br />
''Anticancer Agents Med Chem.'' 2011 Jan;11(1):151-163. <br><br />
<br />
4.'''Nair PC''', Sobhia ME. "Fingerprint directed scaffold hopping for identification of CCR2 antagonists".<br />
''J Chem Inf Model.'' 2008 Sep;48(9):1891-902. <br><br />
<br />
5.'''Nair PC''', Srikanth K, Sobhia ME. "QSAR studies on CCR2 antagonists with chiral sensitive hologram descriptors".<br />
''Bioorg Med Chem Lett.'' 2008 Feb 15;18(4):1323-30. <br><br />
<br />
6.Srikanth K, '''Nair PC''', Sobhia ME. "Probing the structural and topological requirements for CCR2 antagonism: holographic QSAR for <br> indolopiperidine derivatives".''Bioorg Med Chem Lett.'' 2008 Feb 15;18(4):1450-6. <br><br />
<br />
7.'''Nair PC''', Sobhia ME. "Comparative QSTR studies for predicting mutagenicity of nitro compounds".<br />
''J Mol Graph Model.'' 2008 Feb;26(6):916-34. <br><br />
<br />
8.'''Nair PC''', Sobhia ME. "Quantitative structure activity relationship studies on thiourea analogues as influenza virus neuraminidase inhibitors". ''Eur J Med Chem.'' 2008 Feb;43(2):293-9. <br><br />
<br />
9.'''Nair PC''', Sobhia ME."CoMFA based de novo design of pyridazine analogs as PTP1B inhibitors".<br />
''J Mol Graph Model.'' 2007 Jul;26(1):117-23. <br><br />
<br />
== Poster Presentations ==<br />
1.'''Nair PC''', Malde AK, Mark AE."The structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-methyltransferase (PNMT): A Molecular Dynamics and Free Energy study", Molecular Modelling 2010, Melbourne, Australia, 28Nov-1Dec 2010.<br />
<br />
2.'''Nair PC''', Malde AK, Mark AE.Investigating structural requirements for PNMT inhibition: A molecular dynamics and free energy calculation study", Division of chemistry and structural biology symposium, Institute of Molecular Bioscience, Brisbane, Australia, Nov 18-19 2010.<br />
<br />
3.'''Nair PC''', Malde AK, Mark AE. "Investigation of ligand interaction and binding free Energy of 1,2,3,4 tetrahydroisoquinoline analogues as PNMT inhibitors", 61st Indian Pharmaceutical Congress, 11-13 December 2009.<br />
<br />
4.'''Nair PC''', Sobhia ME. "Identification of Novel CCR2 Scaffolds Through Fingerprint Directed Virtual Screening", Virtual Discovery Europe (Computer Aided Drug Design and Screening) London, England, 24-25 October 2007. (Presented by Dr. M. Elizabeth Sobhia, NIPER )<br />
<br />
5.'''Nair PC''', Sobhia ME. "Synergistic application of target structure based alignment and 3D-QSAR study of protein tyrosine phosphatases 1B (PTP1B) inhibitors", Workshop on Pharmcoinformatics: Tools for Drug Target Identification, NIPER, India, March 14-16, 2007.<br />
<br />
6.'''Nair PC''', Sobhia ME. "Quantitative Structure Toxicity Relationship (QSTR) Studies for Predicting Mutagenicity of Nitro Compounds", International Conference on Chemoinformatics, NCL, Pune, India, Jan 22, 2007.<br />
<br />
7.'''Nair PC''', Sobhia ME. "Design of novel PTP1B inhibitors using 3D-QSAR and concept of hypothetical cavity generation", Workshop on Pharmacoinformatics: QSAR, NIPER, India, March 3-4, 2006.<br />
<br />
== Other Conferences/Scientific visits ==<br />
<br />
Molecular Modelling (MM2009), Gold Coast, Queensland, Australia, July 26-29 2009. <br />
<br />
Attended 8th National Center of Competence in Research (NCCR) Practical Course in the area of computational structural biology, Kandersteg, Switzerland, Jan 10-15 2010.<br />
<br />
Visited as a scientific guest in the laboratory of Prof. Wilfred F. van Gunsteren, ETH Zurich, Switzerland, Jan 16-29 2010.<br />
<br />
== Contact Details ==<br />
<br />
Endeavour IPRS Doctoral Fellow <br><br />
Molecular Dynamics Group <br><br />
School of Chemistry and Molecular Biosciences (SCMB) <br><br />
Molecular Biosciences Building (#76) <br><br />
The University of Queensland <br><br />
St. Lucia Campus, Brisbane, QLD 4072 <br><br />
Australia <br><br />
<br />
'''email''' p.nair@uq.edu.au</div>PramodNairhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Pramod_Nair&diff=15903Pramod Nair2011-04-01T12:27:13Z<p>PramodNair: /* Publications */</p>
<hr />
<div>Automated Force Field Topology Builder (ATB) for GROMOS and GROMACS : MD group of Prof. Alan E. Mark<br />
http://compbio.biosci.uq.edu.au/atb/ <br />
<br />
== Research Interests ==<br />
Computer Aided Drug Design (CADD) and Free Energy Calculations<br />
<br />
Alternate Free energy methods to aid high-throughput virtual screening in drug discovery<br />
<br />
Molecular Dynamics simulations of macromolecular and small molecular systems<br />
<br />
== Academic ==<br />
'''B. Pharm.''' Bombay College of Pharmacy, University of Mumbai, India 2001-2005 <br><br />
'''MS (Pharm.)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2005-2007 <br><br />
'''Junior Research Fellow (JRF)''' National Institute of Pharmaceutical Education and Research (NIPER), India 2007-2008 <br><br />
'''PhD Student''' Molecular Dynamics Group, School of Chemistry and Molecular Biosciences (SCMB),University of Queensland, Australia 2009 <br><br />
<br />
== Publications ==<br />
1. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, '''Nair PC''', Oostenbrink C, Mark AE. An Automated force field Topology Builder (ATB) and repository: version 1.0. J Chem Theory Comput. 2011, submitted.<br />
<br />
2.'''Nair PC''', Malde AK, Mark AE."Using theory to reconcile experiment: the structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-MethylTransferase (PNMT)". ''J Chem Theory Comput.'' In press <br><br />
<br />
3.'''Nair PC'''. "Molecular Field Analysis (MFA) and other QSAR techniques in development of phosphatase inhibitors".<br />
''Anticancer Agents Med Chem.'' 2011 Jan;11(1):151-163. <br><br />
<br />
4.'''Nair PC''', Sobhia ME. "Fingerprint directed scaffold hopping for identification of CCR2 antagonists".<br />
''J Chem Inf Model.'' 2008 Sep;48(9):1891-902. <br><br />
<br />
5.'''Nair PC''', Srikanth K, Sobhia ME. "QSAR studies on CCR2 antagonists with chiral sensitive hologram descriptors".<br />
''Bioorg Med Chem Lett.'' 2008 Feb 15;18(4):1323-30. <br><br />
<br />
6.Srikanth K, '''Nair PC''', Sobhia ME. "Probing the structural and topological requirements for CCR2 antagonism: holographic QSAR for <br> indolopiperidine derivatives".''Bioorg Med Chem Lett.'' 2008 Feb 15;18(4):1450-6. <br><br />
<br />
7.'''Nair PC''', Sobhia ME. "Comparative QSTR studies for predicting mutagenicity of nitro compounds".<br />
''J Mol Graph Model.'' 2008 Feb;26(6):916-34. <br><br />
<br />
8.'''Nair PC''', Sobhia ME. "Quantitative structure activity relationship studies on thiourea analogues as influenza virus neuraminidase inhibitors". ''Eur J Med Chem.'' 2008 Feb;43(2):293-9. <br><br />
<br />
9.'''Nair PC''', Sobhia ME."CoMFA based de novo design of pyridazine analogs as PTP1B inhibitors".<br />
''J Mol Graph Model.'' 2007 Jul;26(1):117-23. <br><br />
<br />
== Poster Presentations ==<br />
1.'''Nair PC''', Malde AK, Mark AE."The structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-methyltransferase (PNMT): A Molecular Dynamics and Free Energy study", Molecular Modelling 2010, Melbourne, Australia, 28Nov-1Dec 2010.<br />
<br />
2.'''Nair PC''', Malde AK, Mark AE.Investigating structural requirements for PNMT inhibition: A molecular dynamics and free energy calculation study", Division of chemistry and structural biology symposium, Institute of Molecular Bioscience, Brisbane, Australia, Nov 18-19 2010.<br />
<br />
3.'''Nair PC''', Malde AK, Mark AE. "Investigation of ligand interaction and binding free Energy of 1,2,3,4 tetrahydroisoquinoline analogues as PNMT inhibitors", 61st Indian Pharmaceutical Congress, 11-13 December 2009.<br />
<br />
4.'''Nair PC''', Sobhia ME. "Identification of Novel CCR2 Scaffolds Through Fingerprint Directed Virtual Screening", Virtual Discovery Europe (Computer Aided Drug Design and Screening) London, England, 24-25 October 2007. (Presented by Dr. M. Elizabeth Sobhia, NIPER )<br />
<br />
5.'''Nair PC''', Sobhia ME. "Synergistic application of target structure based alignment and 3D-QSAR study of protein tyrosine phosphatases 1B (PTP1B) inhibitors", Workshop on Pharmcoinformatics: Tools for Drug Target Identification, NIPER, India, March 14-16, 2007.<br />
<br />
6.'''Nair PC''', Sobhia ME. "Quantitative Structure Toxicity Relationship (QSTR) Studies for Predicting Mutagenicity of Nitro Compounds", International Conference on Chemoinformatics, NCL, Pune, India, Jan 22, 2007.<br />
<br />
7.'''Nair PC''', Sobhia ME. "Design of novel PTP1B inhibitors using 3D-QSAR and concept of hypothetical cavity generation", Workshop on Pharmacoinformatics: QSAR, NIPER, India, March 3-4, 2006.<br />
<br />
== Other Conferences/Scientific visits ==<br />
<br />
Molecular Modelling (MM2009), Gold Coast, Queensland, Australia, July 26-29 2009. <br />
<br />
Attended 8th National Center of Competence in Research (NCCR) Practical Course in the area of computational structural biology, Kandersteg, Switzerland, Jan 10-15 2010.<br />
<br />
Visited as a scientific guest in the laboratory of Prof. Wilfred F. van Gunsteren, ETH Zurich, Switzerland, Jan 16-29 2010.<br />
<br />
== Contact Details ==<br />
<br />
Endeavour IPRS Doctoral Fellow <br><br />
Molecular Dynamics Group <br><br />
School of Chemistry and Molecular Biosciences (SCMB) <br><br />
Molecular Biosciences Building (#76) <br><br />
The University of Queensland <br><br />
St. Lucia Campus, Brisbane, QLD 4072 <br><br />
Australia <br><br />
<br />
'''email''' p.nair@uq.edu.au</div>PramodNair