Theoretical Seminars and Journal Club

Schedule

date | main presenter | topic

See the Group meeting schedule.

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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)! - What will be new?

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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