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

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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. (https://doi.org/10.1002/prot.23105)

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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.

ORCID iDs

Palmer, D. S. ORCID logoORCID: https://orcid.org/0000-0003-4356-9144 and Jensen, F.;
  • Item type:Article
    ID code:39167
    Dates:
    Date
    Event
    1 October 2011
    Published
    Subjects:Science > Physics
    Department:Faculty of Science > Physics
    Depositing user: Pure Administrator
    Date deposited:16 Apr 2012 11:00
    Last modified:11 Nov 2024 10:07
    URI:https://strathprints.strath.ac.uk/id/eprint/39167
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