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Biased fragment distribution in MC simulation of protein folding

✍ Scribed by Eric Martineau; Pierre-Jean L'Heureux; John R. Gunn

Publisher: John Wiley and Sons
Year: 2004
Tongue: English
Weight: 194 KB
Volume: 25
Category: Article
ISSN: 0192-8651
DOI: 10.1002/jcc.20109

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✦ Synopsis

Abstract

Monte Carlo (MC) methods play an important role in simulations of protein folding. These methods rely on a random sampling of moves on a potential energy surface. To improve the efficiency of the sampling, we propose a new selection of trial moves based on an empirical distribution of three‐residue (triplet) conformations. This selection is compared to random combinations of the preferred conformations of the three amino acids, and it is shown that the new trial moves lead to finding structures closer to the native conformation. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1895–1903, 2004

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