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Monte Carlo sampling algorithm for searching a scale-transformed energy space of polypeptides

✍ Scribed by Hideaki Nakamura

Publisher: John Wiley and Sons
Year: 2002
Tongue: English
Weight: 131 KB
Volume: 23
Category: Article
ISSN: 0192-8651
DOI: 10.1002/jcc.10034

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✦ Synopsis

Abstract

A Monte Carlo sampling algorithm for searching a scale‐transformed conformational energy space of polypeptides is presented. This algorithm is based on the assumption that energy barriers can be overcome by a uniform sampling of the logarithmically transformed energy space. This algorithm is tested with Met‐enkephalin. For comparison, the entropy sampling Monte Carlo (ESMC) simulation is performed. First, the global minimum is easily found by the optimization of a scale‐transformed energy space. With a new Monte Carlo sampling, energy barriers of 3000 kcal/mol are frequently overcome, and low‐energy conformations are sampled more efficiently than with ESMC simulations. Several thermodynamic quantities are calculated with good accuracy. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 511–516, 2002; DOI 10.1002/jcc.10034

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