Theoretical Seminars and Journal Club: Difference between revisions

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=== The paper pool ===
=== The paper pool ===


30 October 2008,Itamar Kass, Clustering methods [[media:Clustering_methods.pdf| Itamar's clustering talk]] ([[media:Algorithms_for_Clustering_Molecular_Dynamics_Configurations_.pdf| Algorithms for Clustering Molecular Dynamics Configurations]]).
30 October 2008,Itamar Kass, Clustering methods [[media:Clustering_methods.pdf| Itamar's clustering talk]] ([[media:Algorithms_for_Clustering_Molecular_Dynamics_Configurations_.pdf| Algorithms for Clustering Molecular Dynamics Configurations]], [[media:Clustering_molecular_dynamics_trajectories-_I._Characterizing_the_performance_of_different_clustering_algorithms.pdf‎| Clustering molecular dynamics trajectories- I. Characterizing the performance of different clustering algorithms]] and ).

Revision as of 03:31, 30 October 2008

Schedule

date | main presenter | topic


See the Group meeting schedule.



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. AVOIDING SINGULARITIES AND NUMERICAL INSTABILITIES IN FREE-ENERGY CALCULATIONS BASED ON MOLECULAR SIMULATIONS. CHEMICAL PHYSICS LETTERS, 1994, 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 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) Mixture models for protein structure ensembles. Bioinformatics Vol. 24 no. 19 2008, pages 2184–2192.

6. 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

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

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 DOI: 10.1002/anie.200200539

9. Alan D. Sokal (1996) Transgressing the Boundaries: Towards a Transformative Hermeneutics of Quantum Gravity Social Text 46/47, 217-252.


The paper pool

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 ).