Theoretical Seminars and Journal Club: Difference between revisions
No edit summary |
|||
| Line 69: | Line 69: | ||
30 October 2008,Itamar Kass, Clustering methods [[file:Clustering_methods.pdf]]. | 30 October 2008,Itamar Kass, Clustering methods [[file:Clustering_methods.pdf]]. | ||
[[Image: | [[Image:Clustering_methods.pdf]] | ||
Revision as of 03:24, 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 File:Clustering methods.pdf. File:Clustering methods.pdf
