Theoretical Seminars and Journal Club: Difference between revisions
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# 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 | |||
# 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 | |||
# Michael Hirsch and Michael Habeck (2008) [[media:Mixture_models.pdf | Mixture models for protein structure ensembles]]. | |||
http://dx.doi.org/10.1146/annurev.biochem.77.060407.135530 | |||
http://link.aip.org/link/?JCPSA6/72/6035/1 | |||
http://dx.doi.org/10.1002/(SICI)1097-0134(19990901)36:4<542::AID-PROT17>3.0.CO;2-M | |||
''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]]. | |||
''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. | |||
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. | |||
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. | |||
# 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]] | |||
# 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
- 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
- Miller (2006) A Scientist’s Nightmare: Software Problem Leads to Five Retractions Science 314, 1856-1857
- Petsko (2007) And the second shall be first. Genome Biol. 8,103
- 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 |
- 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 - 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
- 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
- Michael Hirsch and Michael Habeck (2008) Mixture models for protein structure ensembles.
Bioinformatics Vol. 24 no. 19 2008, pages 2184–2192.
- 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
- 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
- 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
- Alan D. Sokal (1996) 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
- 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).