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Conformational search of peptides and proteins: Monte Carlo minimization with an adaptive bias method applied to the heptapeptide deltorphin
Author(s) -
Ozkan S. Banu,
Meirovitch Hagai
Publication year - 2004
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.10399
Subject(s) - dihedral angle , monte carlo method , maxima and minima , minification , pentapeptide repeat , energy minimization , chemistry , statistical physics , mathematics , computational chemistry , peptide , physics , mathematical optimization , molecule , statistics , mathematical analysis , hydrogen bond , biochemistry , organic chemistry
The energy function of a protein consists of a tremendous number of minima. Locating the global energy minimum (GEM) structure, which corresponds approximately to the native structure, is a severe problem in global optimization. Recently we have proposed a conformational search technique based on the Monte Carlo minimization (MCM) method of Li and Scheraga, where trial dihedral angles are not selected at random within the range [−180°,180°] (as with MCM) but with biased probabilities depending on the increased structure‐energy correlations as the GEM is approached during the search. This method, called the Monte Carlo minimization with an adaptive bias (MCMAB), was applied initially to the pentapeptide Leu‐enkephalin. Here we study its properties further by applying it to the larger peptide with bulky side chains, deltorphin (H‐Tyr‐D‐Met‐Phe‐His‐Leu‐Met‐Asp‐NH 2 ). We find that on average the number of energy minimizations required by MCMAB to locate the GEM for the first time is smaller by a factor of approximately three than the number required by MCM—in accord with results obtained for Leu‐enkephalin. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 565–572, 2004