Protein Structure Refinement Through Structure Selection and Averaging from Molecular Dynamics Ensembles

Overview

Journal J Chem Theory Comput

Publisher American Chemical Society

Specialties Biochemistry
Chemistry

Date 2013 Mar 26

PMID 23526422

Citations 42

Authors

Vahid Mirjalili

Michael Feig

Affiliations

Soon will be listed here.

Abstract

A molecular dynamics (MD) simulation based protocol for structure refinement of template-based model predictions is described. The protocol involves the application of restraints, ensemble averaging of selected subsets, interpolation between initial and refined structures, and assessment of refinement success. It is found that sub-microsecond MD-based sampling when combined with ensemble averaging can produce moderate but consistent refinement for most systems in the CASP targets considered here.

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