Picture of virus under microscope

Research under the microscope...

The Strathprints institutional repository is a digital archive of University of Strathclyde research outputs.

Strathprints serves world leading Open Access research by the University of Strathclyde, including research by the Strathclyde Institute of Pharmacy and Biomedical Sciences (SIPBS), where research centres such as the Industrial Biotechnology Innovation Centre (IBioIC), the Cancer Research UK Formulation Unit, SeaBioTech and the Centre for Biophotonics are based.

Explore SIPBS research

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.

Full text not available in this repository. (Request a copy from the Strathclyde author)

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.