Evaluating genetic algorithms in protein-ligand docking

  • Authors:

  • Rafael Ördög;Vince Grolmusz

  • Affiliations:

  • Protein Information Technology Group, Eötvös University, Budapest and Uratim Ltd., Nyíregyháza, Hungary;Protein Information Technology Group, Eötvös University, Budapest and Uratim Ltd., Nyíregyháza, Hungary

  • Venue:
  • ISBRA'08 Proceedings of the 4th international conference on Bioinformatics research and applications
  • Year:
  • 2008

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Abstract

In silico protein-ligand docking is a basic problem in pharmaceuticsand bio-informatics research. One of the very few protein-ligand docking software with available source is the Autodock 3.05 of the ScrippsResearch Institute. Autodock 3.05 uses a Lamarckian genetic algorithmfor global optimization with a Solis-Wets local search strategy. In thiswork we evaluate the convergence speed and the deviation properties ofthe solution produced by Autodock with diverse parameter settings. Weconclude that the docking energies found by the genetic algorithm haveuncomfortably large deviations. We also suggest a method for considerablydecreasing the deviation while the number of evaluations will notbe increased.