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Predicting large-scale conformational changes in proteins using energy-weighted normal modes

Palmer, D. S. and Jensen, F. (2011) Predicting large-scale conformational changes in proteins using energy-weighted normal modes. Proteins: Structure, Function, and Bioinformatics, 79 (10). pp. 2778-2793.

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Abstract

We report the development of a method to improve the sampling of protein conformational space in molecular simulations. It is shown that a principal component analysis of energy-weighted normal modes in Cartesian coordinates can be used to extract vectors suitable for describing the dynamics of protein substructures. The method can operate with either atomistic or user-defined coarse-grained models of protein structure. An implicit reverse coarse-graining allows the dynamics of all-atoms to be recovered when a coarse-grained model is used. For an external test set of four proteins, it is shown that the new method is more successful than normal mode analysis in describing the large-scale conformational changes observed on ligand binding. The method has potential applications in protein-ligand and protein-protein docking and in biasing molecular dynamics simulations.

Item type: Article
ID code: 39167
Keywords: normal , mode, vibrational, analysis, protein, conformation, large-scale, frequency, Physics, Medicine(all)
Subjects: Science > Physics
Department: Faculty of Science > Physics
Related URLs:
    Depositing user: Pure Administrator
    Date Deposited: 16 Apr 2012 12:00
    Last modified: 05 Sep 2014 15:45
    URI: http://strathprints.strath.ac.uk/id/eprint/39167

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