Theoretical Seminars and Journal Club: Difference between revisions

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1.  BEUTLER TC, MARK AE, VANSCHAIK RC, et al. AVOIDING SINGULARITIES AND NUMERICAL INSTABILITIES IN FREE-ENERGY CALCULATIONS BASED ON MOLECULAR SIMULATIONS.
# BEUTLER TC, MARK AE, VANSCHAIK RC, et al. (1994) AVOIDING SINGULARITIES AND NUMERICAL INSTABILITIES IN FREE-ENERGY CALCULATIONS BASED ON MOLECULAR SIMULATIONS. ''Chem. Phys. Lett.'' '''222''' (6) : 529-539. <br>http://dx.doi.org/10.1016/0009-2614(94)00397-1
CHEMICAL PHYSICS LETTERS, 1994, 222 (6) : 529-539.  
# Frank Alber, ­ Friedrich Förster, ­ Dmitry Korkin, Maya Topf and ­ Andrej Sali Integrating Diverse Data for Structure Determination of Macromolecular Assemblies. ''Annu. Rev. Biochem.'' http://dx.doi.org/10.1146/annurev.biochem.77.060407.135530
http://dx.doi.org/10.1016/0009-2614(94)00397-1
# Tropp J. (1980) Dipolar relaxation and nuclear Overhauser effects in nonrigid molecules: The effect of fluctuating internuclear distances. ''J. Chem. Phys.'' '''72''', 6035. http://link.aip.org/link/?JCPSA6/72/6035/1
 
# Daura X, Antes I, van Gunsteren WF, Thiel W, Mark AE. (1999) The effect of motional averaging on the calculation of NMR-derived structural properties. ''Proteins'' '''36'''(4), 542-55. http://dx.doi.org/10.1002/(SICI)1097-0134(19990901)36:4<542::AID-PROT17>3.0.CO;2-M
2. Frank Alber, ­ Friedrich Förster, ­ Dmitry Korkin, Maya Topf and ­ Andrej Sali Integrating Diverse Data for Structure Determination of Macromolecular Assemblies
# Michael Hirsch and Michael Habeck (2008) [[media:Mixture_models.pdf | Mixture models for protein structure ensembles]].
Annual Review of Biochemistry
http://dx.doi.org/10.1146/annurev.biochem.77.060407.135530
 
3. Tropp J. (1980) Dipolar relaxation and nuclear Overhauser effects in nonrigid molecules: The effect of fluctuating internuclear distances. ''J. Chem. Phys.'' '''72''', 6035
http://link.aip.org/link/?JCPSA6/72/6035/1
 
4. Daura X, Antes I, van Gunsteren WF, Thiel W, Mark AE. (1999) The effect of motional averaging on the calculation of NMR-derived structural properties. ''Proteins'' '''36'''(4), 542-55
http://dx.doi.org/10.1002/(SICI)1097-0134(19990901)36:4<542::AID-PROT17>3.0.CO;2-M
 
5. Michael Hirsch and Michael Habeck (2008) [[media:Mixture_models.pdf | Mixture models for protein structure ensembles]].
''Bioinformatics'' Vol. 24 no. 19 2008, pages 2184–2192.
''Bioinformatics'' Vol. 24 no. 19 2008, pages 2184–2192.
 
# Wolfgang Rieping, Michael Habeck and Michael Nilges (2005) [[media:Modeling_errors_in_NOE.pdf | Modeling Errors in NOE Data with a Log-normal Distribution Improves the Quality of NMR Structures]].
6. Wolfgang Rieping, Michael Habeck and Michael Nilges (2005) [[media:Modeling_errors_in_NOE.pdf | Modeling Errors in NOE Data with a Log-normal Distribution Improves the Quality of NMR Structures]].
''JACS'', '''127''', 16026-16027
''JACS'', '''127''', 16026-16027
 
# Davis A, St-Gallay SA, Kleywegt GJ. "Limitations and lessons in the use of X-ray structural information in drug design". Drug Discovery Today, 2008, 19/20, 831.  
7. Davis A, St-Gallay SA, Kleywegt GJ. "Limitations and lessons in the use of X-ray structural information in drug design". Drug Discovery Today, 2008, 19/20, 831.  
http://dx.doi.org/10.1016/j.drudis.2008.06.006
http://dx.doi.org/10.1016/j.drudis.2008.06.006
 
# Davis AM, Teague SJ, Kleywegt GJ. "Application and Limitations of X-ray crystallographic data in structure-based ligand and drug design". Angew. Chem. Intl. Ed., 2003, 42, 2718.  
8. Davis AM, Teague SJ, Kleywegt GJ. "Application and Limitations of X-ray crystallographic data in structure-based ligand and drug design". Angew. Chem. Intl. Ed., 2003, 42, 2718.  
http://www3.interscience.wiley.com/cgi-bin/fulltext/104539506/PDFSTART  
http://www3.interscience.wiley.com/cgi-bin/fulltext/104539506/PDFSTART  
DOI: 10.1002/anie.200200539
DOI: 10.1002/anie.200200539
 
# Alan D. Sokal (1996) [[media:Sokal-transgressing-boundaries.pdf | Transgressing the Boundaries: Towards a Transformative Hermeneutics of Quantum Gravity]] ''Social Text'' '''46/47''', 217-252.
9. Alan D. Sokal (1996) [[media:Sokal-transgressing-boundaries.pdf | Transgressing the Boundaries: Towards a Transformative Hermeneutics of Quantum Gravity]] ''Social Text'' '''46/47''', 217-252.
# Ma JP, 2005 , Structure, [[media:Usefulness_and_Limitations_of_Normal_Mode_Analysis_in_Modeling_Dynamics_of_Biomolecular_Complexes.pdf]]
 
# Kitao A and GO N, 1999, current opinion in structural biology. [[media:Investigating_protein_dynamics_in_collective_coordinate_space.pdf]]
10. Ma JP, 2005 , Structure, [[media:Usefulness_and_Limitations_of_Normal_Mode_Analysis_in_Modeling_Dynamics_of_Biomolecular_Complexes.pdf]]
# Hess B, 2002, Physical review E. [[media:Convergence_of_sampling_in_protein_simulations.pdf ]]
 
11. Kitao A and GO N, 1999, current opinion in structural biology. [[media:Investigating_protein_dynamics_in_collective_coordinate_space.pdf]]
 
12. Hess B, 2002, Physical review E. [[media:Convergence_of_sampling_in_protein_simulations.pdf ]]
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Revision as of 23:50, 22 March 2009

Schedule

date | main presenter | topic


See the Group meeting schedule.



Papers for the Next Journal Club

  1. Chang et al. (2001) Structure of MsbA from E. coli: A Homolog of the Multidrug Resistance ATP Binding Cassette (ABC) Transporters. Science 293, 1793-1800
  2. Miller (2006) A Scientist’s Nightmare: Software Problem Leads to Five Retractions Science 314, 1856-1857
  3. Petsko (2007) And the second shall be first. Genome Biol. 8,103
  4. Jeffrey (2009) Analysis of errors in the structure determination of MsbA Acta Crystallogr. D65, 193–199

Suggested Topics

name of topic | suggestion by


1. Soft Core non-bonded interactions - Alpesh

2. Structural Determination - Mitchell

3. How to define Clusters and what can we learn from it on proteins properties? - Itamar

4. Gromacs 4: What's new - What's broken?

Breaking the 2fs time step barrier and clever parallelisation.

5. GROMOS2017 - Coming soon(ish)! - New developments

6. Error in Crystal Structures and its implications. Can MD be used for X-ray structure refinement?


The paper pool

Author | Title | Topic area | DOI URL |


  1. BEUTLER TC, MARK AE, VANSCHAIK RC, et al. (1994) AVOIDING SINGULARITIES AND NUMERICAL INSTABILITIES IN FREE-ENERGY CALCULATIONS BASED ON MOLECULAR SIMULATIONS. Chem. Phys. Lett. 222 (6) : 529-539.
    http://dx.doi.org/10.1016/0009-2614(94)00397-1
  2. Frank Alber, ­ Friedrich Förster, ­ Dmitry Korkin, Maya Topf and ­ Andrej Sali Integrating Diverse Data for Structure Determination of Macromolecular Assemblies. Annu. Rev. Biochem. http://dx.doi.org/10.1146/annurev.biochem.77.060407.135530
  3. Tropp J. (1980) Dipolar relaxation and nuclear Overhauser effects in nonrigid molecules: The effect of fluctuating internuclear distances. J. Chem. Phys. 72, 6035. http://link.aip.org/link/?JCPSA6/72/6035/1
  4. Daura X, Antes I, van Gunsteren WF, Thiel W, Mark AE. (1999) The effect of motional averaging on the calculation of NMR-derived structural properties. Proteins 36(4), 542-55. http://dx.doi.org/10.1002/(SICI)1097-0134(19990901)36:4<542::AID-PROT17>3.0.CO;2-M
  5. Michael Hirsch and Michael Habeck (2008) Mixture models for protein structure ensembles.

Bioinformatics Vol. 24 no. 19 2008, pages 2184–2192.

  1. Wolfgang Rieping, Michael Habeck and Michael Nilges (2005) Modeling Errors in NOE Data with a Log-normal Distribution Improves the Quality of NMR Structures.

JACS, 127, 16026-16027

  1. Davis A, St-Gallay SA, Kleywegt GJ. "Limitations and lessons in the use of X-ray structural information in drug design". Drug Discovery Today, 2008, 19/20, 831.

http://dx.doi.org/10.1016/j.drudis.2008.06.006

  1. Davis AM, Teague SJ, Kleywegt GJ. "Application and Limitations of X-ray crystallographic data in structure-based ligand and drug design". Angew. Chem. Intl. Ed., 2003, 42, 2718.

http://www3.interscience.wiley.com/cgi-bin/fulltext/104539506/PDFSTART DOI: 10.1002/anie.200200539

  1. Alan D. Sokal (1996) Transgressing the Boundaries: Towards a Transformative Hermeneutics of Quantum Gravity Social Text 46/47, 217-252.
  2. Ma JP, 2005 , Structure, media:Usefulness_and_Limitations_of_Normal_Mode_Analysis_in_Modeling_Dynamics_of_Biomolecular_Complexes.pdf
  3. Kitao A and GO N, 1999, current opinion in structural biology. media:Investigating_protein_dynamics_in_collective_coordinate_space.pdf
  4. Hess B, 2002, Physical review E. media:Convergence_of_sampling_in_protein_simulations.pdf

The Theoretical Seminars Lectures

30 October 2008,Itamar Kass, Clustering methods Itamar's clustering talk ( Algorithms for Clustering Molecular Dynamics Configurations, Clustering molecular dynamics trajectories- I. Characterizing the performance of different clustering algorithms and Peptide Folding- When Simulation Meets Experiment).