Theoretical Seminars and Journal Club
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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.
Link here - Frank Alber, Friedrich Förster, Dmitry Korkin, Maya Topf and Andrej Sali Integrating Diverse Data for Structure Determination of Macromolecular Assemblies. Annu. Rev. Biochem.
Link here - Tropp J. (1980) Dipolar relaxation and nuclear Overhauser effects in nonrigid molecules: The effect of fluctuating internuclear distances. J. Chem. Phys. 72, 6035.
Link here - 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.
- Michael Hirsch and Michael Habeck (2008) Mixture models for protein structure ensembles.Bioinformatics Vol. 24 no. 19 2008, 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.
Link here - 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.
Link here
DOI: 10.1002/anie.200200539 Link here] - 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
- Aloy P. and Russell R.B. (2006) Structural systems biology: modelling protein interactions. Nat. Rev. Mol. Cell. Biol. 7(3), 188-197.
- Zaccai G. (2000) How soft is a protein? A protein dynamics force constant measured by neutron scattering. Science 288 (5471), 1604-1607.
The Theoretical Seminars Lectures
- Clustering methods (Itamar Kass, 30.10.08)
- PDF file of the talk here (pdf file)
- Complementary reading:
- Torda, AE and van Gunsrteren, WF (1994) Algorithms for clustering molecular dynamics configurations. J. Comput. Chem. 15 (12), 1331-1340
- Shao, J et al (2007) Clustering molecular dynamics trajectories: 1. Characterizing the performance of different clustering algorithms. J. Chem. Theory Comput. 3, 2312-2334
- Daura, X et al (1999) Peptide folding: when simulation meets experiment. Angew. Chem. Int. Ed. '38 (1/2), 236-240