Help and Information Page for Normal Modes Analysis (NMA) of Protein Motions and Flexibility Prediction Tool
This help page is currently under construction (Winter, 2005).This tool allows the user to upload a query structure (or choose it from the motions database), calculate its 5 lowest frequency Normal Modes, build the movies of these vibrations and compare them with the pre-calculated flexibility regions based on either multiple structural alignment for the corresponding fold family (for single-domain queries) or supplied B-factors. If B-factors are not supplied, they are taken from the closest sequence match in Astral database.
[International users: This document is available in Spanish, French, German, Italian, and Portuguese translations.]
Copyright Statement
Unless otherwise notated, NMA page and all underlying code are copyright 2003, Vadim Alexandron and Mark Gerstein, all rights reserved. Please use the citation below when refering in print to the results obtained by this tool.The (current) citation for the NMA and Flexibility Tool
Other Papers
- M Gerstein, A Lesk, C Chothia (1994). "Structural Mechanisms for Domain Movements in Proteins," Biochemistry 33: 6739-6749.
- Review describing protein motions: M Gerstein, R Jansen, T Johnson, J Tsai & W Krebs (1999). "Studying Macromolecular Motions in a Database Framework: from Structure to Sequence," Rigidity theory and applications (ed. M F Thorpe & P M Duxbury, Kluwer Academic/Plenum Publishers), pp. 401-442. [full-text]
- Paper in MIE: WG Krebs, J Tsai, V Alexandrov, N Echols, J Junker, R Jansen and M Gerstein (2001), "Studying Protein Flexibility in a Statistical Framework: Tools and Databases for Analyzing Structures and Approaches for Mapping this onto Sequences," Methods in Enzymology (in press). [full-text]
Authors
The authors of this NMA and Flexibility Tool are Mark Gerstein and Vadim Alexandrov. The contributions of Nat Echols and Duncan Milburn are acknowledged.![[home]](/molmovdb/gif/home-icon.gif){kind=icon}
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Copyright (C) 2003 Vadim Alexandrov
and Mark Gerstein. |