ISSN:
0192-8651
Keywords:
optimization method
;
global minimum-energy conformations
;
polypeptides
;
conformational space annealing
;
Chemistry
;
Theoretical, Physical and Computational Chemistry
Source:
Wiley InterScience Backfile Collection 1832-2000
Topics:
Chemistry and Pharmacology
,
Computer Science
Notes:
A new optimization method is presented to search for the global minimum-energy conformations of polypeptides. The method combines essential aspects of the build-up procedure and the genetic algorithm, and it introduces the important concept of “conformational space annealing.” Instead of considering a single conformation, attention is focused on a population of conformations while new conformations are obtained by modifying a “seed conformation.” The annealing is carried out by introducing a distance cutoff, Dcut, which is defined in the conformational space; Dcut effectively divides the whole conformational space of local minima into subdivisions. The value of Dcut is set to a large number at the beginning of the algorithm to cover the whole conformational space, and annealing is achieved by slowly reducing it. Many distinct local minima designed to be distributed as far apart as possible in conformational space are investigated simultaneously. Therefore, the new method finds not only the global minimum-energy conformation but also many other distinct local minima as by-products. The method is tested on Met-enkephalin, a 24-dihedral angle problem. For all 100 independent runs, the accepted global minimum-energy conformation was obtained after about 2600 minimizations on average. © 1997 John Wiley & Sons, Inc. J Comput Chem 18: 1222-1232
Additional Material:
5 Ill.
Type of Medium:
Electronic Resource
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