Journal of Computer-Aided Molecular Design

, Volume 11, Issue 3, pp 209–228 | Cite as

A comparison of heuristic search algorithms for molecular docking

  • David R. Westhead
  • David E. Clark
  • Christopher W. Murray
Article

Abstract

This paper describes the implementation and comparison of four heuristic search algorithms (genetic algorithm, evolutionary programming, simulated annealing and tabu search) and a random search procedure for flexible molecular docking. To our knowledge, this is the first application of the tabu search algorithm in this area. The algorithms are compared using a recently described fast molecular recognition potential function and a diverse set of five protein–ligand systems. Statistical analysis of the results indicates that overall the genetic algorithm performs best in terms of the median energy of the solutions located. However, tabu search shows a better performance in terms of locating solutions close to the crystallographic ligand conformation. These results suggest that a hybrid search algorithm may give superior results to any of the algorithms alone.

Ligand–protein docking Molecular recognition Evolutionary algorithms Simulated annealing Tabu search 

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Copyright information

© Kluwer Academic Publishers 1997

Authors and Affiliations

  • David R. Westhead
    • 1
  • David E. Clark
    • 1
  • Christopher W. Murray
    • 1
  1. 1.Proteus Molecular Design Ltd., Proteus HouseCheshireU.K.

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