Theoretical Seminars
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Schedule
See the Group meeting schedule.
Next Theoretical Seminar: TBA (Alpesh Malde, 21.05.09)
- Papers that would be good to read: TBA
Suggested topics
You are more than welcome to suggest topics for future theoretical seminars.
Name of topic | Suggestion by
- Soft Core non-bonded interactions | Alpesh
- Structural Determination | Mitchell
- How to define Clusters and what can we learn from it on proteins properties? | Itamar — Done
- Gromacs 4: What's new - What's broken? Breaking the 2fs time step barrier and clever parallelisation.
- GROMOS2017 – New developments (Coming soon(ish)!)
- Error in Crystal Structures and its implications. Can MD be used for X-ray structure refinement?
- SETTLE/RATTLE/timestep: methods for the simulation of water, implications in our simulations in a world that thinks the 2-fs timestep is because of the C–H bond vibration frequency.
- LINCS/SHAKE/dummy atoms
- What can be analyzed from simulations? An introduction to the various structural/dynamic properties that can be calculated
- NMA/PCA/ED: what are these methods? how good are they? what for?
- Sequence alignment, prediction of secondary structures, homology modelling
- Of the history of MD: differences between all these forcefields that we always talk about: GROMOS, CHARMM, OPLS, AMBER, GROMACS, GAFF...
- Molecular surfaces, NAccess
Past Theoretical Seminars
Determination of secondary structure elements (David Poger, 23.04.09)
- PDF file of the talk here
- Complementary reading:
- Kabsch, W and Sander, C (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22 (12), 2577-2637: article of reference for DSSP
- Frishman, D and Argos, P (1995) Knowledge-based protein secondary structure assignment. Proteins 23 (4), 566-579: article of reference for STRIDE
- Sklenar, H, Etchebest, C and Lavery, R (1989) Describing protein structure: a general algorithm yielding complete helicoidal parameters and a unique overall axis. Proteins 6 (1), 46-60: algorithm P-Curve
- Martin, J, Letellier, G, Marin, A, Taly, J-F, de Brevern, AG, Gibrat JF (2005) Protein secondary structure assignment revisited: a detailed analysis of different assignment methods. BMC Struct. Biol. 5, 17.
Clustering methods (Itamar Kass, 30.10.08)
- PDF file of the talk here
- 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