Coupling an Ensemble of Homologues Improves Refinement of Protein Homology Models.

J Chem Theory Comput

ICS-6: Structural Biochemistry, Institute of Complex Systems, Forschungszentrum Jülich , 52425 Jülich, Germany.

Published: December 2015

Atomic models of proteins built by homology modeling or from low-resolution experimental data may contain considerable local errors. The refinement success of molecular dynamics simulations is usually limited by both force field accuracy and by the substantial width of the conformational distribution at physiological temperatures. We propose a method to overcome both these problems by coupling homologous replicas during a molecular dynamics simulation, which narrows the conformational distribution, and smoothens and even improves the energy landscape by adding evolutionary information.

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http://dx.doi.org/10.1021/acs.jctc.5b00942DOI Listing

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