A CRITICAL COMPARISON OF SEARCH ALGORITHMS APPLIED TO THE OPTIMIZATION OF PROTEIN SIDE-CHAIN CONFORMATIONS

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.