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.Full text not available in this repository. (Request a copy from the Strathclyde author)
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.
|Keywords:||normal , mode, vibrational, analysis, protein, conformation, large-scale, frequency, Physics, Medicine(all)|
|Subjects:||Science > Physics|
|Department:||Faculty of Science > Physics|
|Depositing user:||Pure Administrator|
|Date Deposited:||16 Apr 2012 11:00|
|Last modified:||05 May 2016 00:22|