A COMPARISON OF HEURISTIC-SEARCH ALGORITHMS FOR MOLECULAR DOCKING

This paper describes the implementation and comparison of four heurist ic search algorithms (genetic algorithm, evolutionary programming, sim ulated annealing and tabu search) and a random search procedure for fl exible molecular docking. To our knowledge, this is the first applicat ion of the tabu search algorithm in this area. The algorithms are comp ared using a recently described fast molecular recognition potential f unction and a diverse set of five protein-ligand systems. Statistical analysis of the results indicates that overall the genetic algorithm p erforms best in terms of the median energy of the solutions located. H owever, tabu search shows a better performance in terms of locating so lutions close to the crystallographic ligand conformation. These resul ts suggest that a hybrid search algorithm may give superior results to any of the algorithms alone.