Theoretical Seminars: Difference between revisions
From MDWiki
Jump to navigationJump to search
No edit summary |
|||
| Line 7: | Line 7: | ||
* Papers that would be good to read: | * Papers that would be good to read: | ||
*# [[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- | *# [[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: | * 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.]] | ||
== Suggested topics == | == Suggested topics == | ||
Revision as of 01:58, 28 March 2009
Schedule
See the Group meeting schedule.
Next Theoretical Seminar: Prediction of secondary structures (David Poger, 16.04.09)
- Papers that would be good to read:
- 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
- Other papers:
- 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.
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?
Past Theoretical Seminars
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
