Journal
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
Volume 79, Issue 10, Pages 2778-2793Publisher
WILEY
DOI: 10.1002/prot.23105
Keywords
harmonic vibrational docking sampling molecular dynamics
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Funding
- Vilium Kahn Rasmussen foundation
- Danish Center for Scientific Computing
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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.
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