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Three variations of genetic algorithm for searching biomolecular conformation space: Comparison of GAP 1.0, 2.0, and 3.0
Author(s) -
Jin A. Y.,
Leung F. Y.,
Weaver D. F.
Publication year - 1999
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(199910)20:13<1329::aid-jcc1>3.0.co;2-h
Subject(s) - conformational isomerism , a priori and a posteriori , force field (fiction) , space (punctuation) , variety (cybernetics) , algorithm , computer science , statistical physics , physics , molecule , artificial intelligence , quantum mechanics , philosophy , epistemology , operating system
Three genetic algorithm programs, GAP 1.0, 2.0, and 3.0, were used in conjunction with the ECEPP/2 force field to search the conformation space of [Met]‐enkephalin. Each program was proficient at quickly finding many diverse low‐energy conformers. Conformer populations displayed a variety of secondary structure motifs including those likely to bind to the μ‐opioid receptor. Limitations in the program's sampling behavior are discussed and method improvements are suggested. Although still in a developmental stage, the GAP programs represent a useful addition to conformational search techniques when no a priori structural information is available. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 1329–1342, 1999