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Energy minimizations with a combination of two knowledge-based potentials for protein folding

✍ Scribed by David de Sancho; Antonio Rey

Publisher
John Wiley and Sons
Year
2008
Tongue
English
Weight
649 KB
Volume
29
Category
Article
ISSN
0192-8651

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✦ Synopsis

Abstract

New force fields that are both simple and accurate are needed for computationally efficient molecular simulation studies to give insight into the actual features of the protein folding process. In this work, we assess a force field based on a new combination of two coarse‐grained potentials taken from the bibliography. These potentials have already been proved efficient in representing different types of interactions, namely the side‐chain interactions and the backbone hydrogen bonds. Now we combine them weighing their contribution to the global energy with a very simplified parameterization. To assess this combination of potentials, we use our evolutionary method to carry out energy minimization experiments for a set of all‐α, all‐β, and (α + β) protein structures. Our results, based on the assembly of short rigid native fragments, suggest that this combination of potentials can be successfully employed in coarse‐grained folding simulations. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2008

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