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A critical comparison of search algorithms applied to the optimization of protein side‐chain conformations
Author(s) -
Tufféry P.,
Etchebest C.,
Hazout S.,
Lavery R.
Publication year - 1993
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.540140705
Subject(s) - simulated annealing , algorithm , heuristic , globular protein , computer science , simple (philosophy) , set (abstract data type) , genetic algorithm , side chain , chain (unit) , mathematical optimization , adaptive simulated annealing , mathematics , chemistry , crystallography , physics , polymer , epistemology , philosophy , organic chemistry , astronomy , programming language
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.