Theoretical Seminars: Difference between revisions

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*# [[media:Kabsch_Biopolymers83.pdf|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
*# [[media:Kabsch_Biopolymers83.pdf|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
*# [[media:Frishman_Proteins95.pdf|Frishman, D and Argos, P (1995) Knowledge-based protein secondary structure assignment. ''Proteins'' '''23''' (4), 566-579]]: article of reference for STRIDE
*# [[media:Frishman_Proteins95.pdf|Frishman, D and Argos, P (1995) Knowledge-based protein secondary structure assignment. ''Proteins'' '''23''' (4), 566-579]]: article of reference for STRIDE
* Other papers:
*# [[media:Sklenar_Proteins89.pdf|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
*# [[media:Sklenar_Proteins89.pdf|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
*# [[media:Martin_BMCStructBiol05.pdf|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.]]
*# [[media:Martin_BMCStructBiol05.pdf|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.]]

Revision as of 07:31, 23 April 2009

Schedule

See the Group meeting schedule.


Next Theoretical Seminar: Prediction of secondary structures (David Poger, 23.04.09)

Suggested topics

You are more than welcome to suggest topics for future theoretical seminars.

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 — Done
  4. Gromacs 4: What's new - What's broken? Breaking the 2fs time step barrier and clever parallelisation.
  5. GROMOS2017 – New developments (Coming soon(ish)!)
  6. Error in Crystal Structures and its implications. Can MD be used for X-ray structure refinement?
  7. 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.
  8. LINCS/SHAKE/dummy atoms
  9. What can be analyzed from simulations? An introduction to the various structural/dynamic properties that can be calculated
  10. NMA/PCA/ED: what are these methods? how good are they? what for?
  11. Sequence alignment, prediction of secondary structures, homology modelling
  12. Of the history of MD: differences between all these forcefields that we always talk about: GROMOS, CHARMM, OPLS, AMBER, GROMACS, GAFF...
  13. Molecular surfaces, NAccess

Past Theoretical Seminars

Determination of secondary structure elements (David Poger, 23.04.09)

Clustering methods (Itamar Kass, 30.10.08)