[gmx-users] Help: Analysis large interdomain motion
feenstra at few.vu.nl
Fri May 20 10:22:15 CEST 2005
> Hi Zhenting Gao,
> Actually, this is not uncommon. The analysis you probably want to
> perform here includes principal components analysis and subsequently
> running the program DynDom to reveal the nature of interdomain motions.
I've tried to develop a method that collects dyndom analysis of several
simulations and/or essential dynamics eigenvectors. It was published as
a book chapter:
K. Anton Feenstra and Herman J. C. Berendsen. "The domain
decomposition of a single-domain protein." in: Monte Carlo approach to
biopolymers and protein folding. pp. 255-267. Eds. P. Grassberger, G.T.
Barkema and W. Nadler, Höchstleistungsrechenzentrum Jülich, Germany;
World Scientific, London, 1998.
I may add that DynDom was developed by Steve Hayward, here are some
references (taken from www.ccp4.ac.uk/ccp4/html/REFERENCES.html):
S.Hayward, A.Kitao, H.J.C.Berendsen, Model-Free Methods of
Analyzing Domain Motions in Proteins from Simulation: A Comparison of
Normal Mode Analysis and Molecular Dynamics Simulation of Lysozyme
Proteins, Structure, Function and Genetics, 27, 425, 1997.
* DynDom main reference:
S.Hayward, H.J.C.Berendsen, Systematic Analysis of Domain Motions
in Proteins from Conformational Change; New Results on Citrate Synthase
and T4 Lysozyme Proteins, Structure, Function and Genetics, 30, 144, 1998.
B.L.de Groot, S.Hayward, D.van Aalten, A.Amadei, H.J.C.Berendsen,
Domain Motions in Bacteriophage T4 Lysozyme; a Comparison between
Molecular Dynamics and Crystallographic Data Proteins, Structure,
Function and Genetics, 31, 116, 1998.
D.Roccatano, A.E.Mark,S.Hayward,Investigation of the Mechanism of
Domain Closure in Citrate Synthase by Molecular Dynamics Simulation J.
Mol. Biol. , 310, 1039, 2001.
* NOTE: New Phone & Fax numbers (below) *
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| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands |
| \_/ \_/ | | | Tel: +31 20 59 87608 - Fax: +31 20 59 87610 |
| | Feenstra at few.vu.nl - www.few.vu.nl/~feenstra/ |
| | "If You See Me Getting High, Knock Me Down" (RHCP) |
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