Pramod Nair

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Automated Force Field Topology Builder (ATB) for GROMOS and GROMACS : MD group of Prof. Alan E. Mark

Research Interests

Computer Aided Drug Design (CADD) and Free Energy Calculations

Alternate Free energy methods to aid high-throughput virtual screening in drug discovery

Molecular Dynamics simulations of macromolecular and small molecular systems


B. Pharm. Bombay College of Pharmacy, University of Mumbai, India 2001-2005
MS (Pharm.) National Institute of Pharmaceutical Education and Research (NIPER), India 2005-2007
Junior Research Fellow (JRF) National Institute of Pharmaceutical Education and Research (NIPER), India 2007-2008
PhD Student Molecular Dynamics Group, School of Chemistry and Molecular Biosciences (SCMB),University of Queensland, Australia 2009


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. DOI: 10.1021/ml300015u PDBcode 4DM3

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.DOI: 10.1021/ct200196m

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. DOI:10.1063/1.3604534

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. DOI: 10.1021/ct1007229

5.Nair PC. "Molecular Field Analysis (MFA) and other QSAR techniques in development of phosphatase inhibitors". Anti-Cancer Agents in Medicinal Chemistry 2011 Jan;11(1):151-163. (Invited Review Article) DOI: 10.2174/187152011794941181

6.Nair PC, Sobhia ME. "Fingerprint directed scaffold hopping for identification of CCR2 antagonists". Journal of Chemical Information and Modeling 2008 Sep;48(9):1891-902. DOI: 10.1021/ci800157j

7.Nair PC, Srikanth K, Sobhia ME. "QSAR studies on CCR2 antagonists with chiral sensitive hologram descriptors". Bioorganic & Medicinal Chemistry Letters 2008 Feb;18(4):1323-30. DOI: 10.1016/j.bmcl.2008.01.023

8.Srikanth K, Nair PC, Sobhia ME. "Probing the structural and topological requirements for CCR2 antagonism: holographic QSAR for
indolopiperidine derivatives".Bioorganic & Medicinal Chemistry Letters 2008 Feb;18(4):1450-6. DOI: 10.1016/j.bmcl.2007.12.072

9.Nair PC, Sobhia ME. "Comparative QSTR studies for predicting mutagenicity of nitro compounds". Journal of Molecular Graphics and Modelling 2008 Feb;26(6):916-34. DOI:10.1016/j.jmgm.2007.06.006

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. DOI: 10.1016/j.ejmech.2007.03.020

11.Nair PC, Sobhia ME."CoMFA based de novo design of pyridazine analogs as PTP1B inhibitors". Journal of Molecular Graphics and Modelling 2007 Jul;26(1):117-23. DOI: 10.1016/j.jmgm.2006.10.002

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)

Poster Presentations

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

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.

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.

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.

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 )

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.

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.

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.

Other Conferences/Scientific visits

Structural Biology Symposium, Institute for Glycomics, Griffith University, Gold Coast, Australia, 2009.

Molecular Modelling (MM2009), Gold Coast, Queensland, Australia, July 26-29 2009.

Attended 8th National Center of Competence in Research (NCCR) Practical Course in the area of computational structural biology, Kandersteg, Switzerland, Jan 10-15 2010.

Visited as a scientific guest in the laboratory of Prof. Wilfred F. van Gunsteren, ETH Zurich, Switzerland, Jan 16-29 2010.

Contact Details

Endeavour IPRS Doctoral Fellow
Molecular Dynamics Group
School of Chemistry and Molecular Biosciences (SCMB)
Molecular Biosciences Building (#76)
The University of Queensland
St. Lucia Campus, Brisbane, QLD 4072