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New optimization method for conformational energy calculations on polypeptides: Conformational space annealing
Author(s) -
Lee Jooyoung,
Scheraga Harold A.,
Rackovsky S.
Publication year - 1997
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/(sici)1096-987x(19970715)18:9<1222::aid-jcc10>3.0.co;2-7
Subject(s) - maxima and minima , dihedral angle , simulated annealing , conformational ensembles , space (punctuation) , global optimization , chemistry , crystallography , computational chemistry , algorithm , computer science , molecular dynamics , mathematics , molecule , hydrogen bond , mathematical analysis , organic chemistry , operating system
Abstract A new optimization method is presented to search for the globalminimum‐energy conformations of polypeptides. The method combines essentialaspects of the build‐up procedure and the genetic algorithm, and itintroduces the important concept of “conformational spaceannealing.” Instead of considering a single conformation, attentionis focused on a population of conformations while new conformations areobtained by modifying a “seed conformation.” The annealing iscarried out by introducing a distance cutoff, D cut , whichis defined in the conformational space; D cut effectivelydivides the whole conformational space of local minima into subdivisions.The value of D cut is set to a large number at thebeginning of the algorithm to cover the whole conformational space, andannealing is achieved by slowly reducing it. Many distinct local minimadesigned to be distributed as far apart as possible in conformational spaceare investigated simultaneously. Therefore, the new method finds not onlythe global minimum‐energy conformation but also many other distinct localminima as by‐products. The method is tested on Met‐enkephalin, a24‐dihedral angle problem. For all 100 independent runs, the acceptedglobal minimum‐energy conformation was obtained after about 2600minimizations on average. © 1997 John Wiley & Sons, Inc. J Comput Chem 18: 1222–1232