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A critical comparison of search algorithms applied to the optimization of protein side-chain conformations

✍ Scribed by P. Tufféry; C. Etchebest; S. Hazout; R. Lavery

Publisher: John Wiley and Sons
Year: 1993
Tongue: English
Weight: 866 KB
Volume: 14
Category: Article
ISSN: 0192-8651
DOI: 10.1002/jcc.540140705

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✦ Synopsis

Abstract

Three different optimization algorithms are applied to solving the problem of finding the best side‐chain conformations with a test set of 14 globular proteins having known crystallographic conformations. It is shown that simulated annealing, simple and modified genetic algorithms, and a heuristic combinatorial approach achieve similar optimal solutions, with the exception of simulated annealing applied to the largest proteins. The efficiency of the different algorithms, however, shows wide variations. General conclusions are drawn concerning the optimal approach to such problems. © 1993 John Wiley & Sons, Inc.

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