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On the Efficiency of Local Search Methods for the Molecular Docking Problem

  • Jorge Tavares
  • Salma Mesmoudi
  • El-Ghazali Talbi
Part of the Lecture Notes in Computer Science book series (LNCS, volume 5483)

Abstract

Evolutionary approaches to molecular docking typically hybridize with local search methods, more specifically, the Solis-Wet method. However, some studies indicated that local search methods might not be very helpful in the context of molecular docking. An evolutionary algorithm with proper genetic operators can perform equally well or even outperform hybrid evolutionary approaches. We show that this is dependent on the type of local search method. We also propose an evolutionary algorithm which uses the L-BFGS method as local search. Results demonstrate that this hybrid evolutionary outperforms previous approaches and is better suited to serve as a basis for evolutionary docking methods.

Keywords

Local Search Evolutionary Algorithm Protein Data Bank Molecular Docking Genetic Operator 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2009

Authors and Affiliations

  • Jorge Tavares
    • 1
  • Salma Mesmoudi
    • 2
  • El-Ghazali Talbi
    • 2
  1. 1.Massachusetts Institute of TechnologyCambridgeUSA
  2. 2.INRIA Lille - Nord Europe Research CentreVilleneuve d’AscqFrance

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