Comparative Study of the Efficiency of Three Protein-Ligand Docking Programs
Abdelouahab Chikhi* and Abderrahmane Bensegueni
Laboratory of Theoretical Chemistry, Department of Chemistry. Faculty of Sciences, Mentouri University,Constantine, Algeria
Laboratory of Microbiological Applications, Department of Biochemistry-Microbiology. Faculty of natural and life Sciences, Mentouri University, Constantine, Algeria
- *Corresponding Author:
- Dr. Abdelouahab
Laboratory of Theoretical Chemistry
Department of Chemistry. Faculty of Sciences
Mentouri University, Constantine, Algeria
Tel : + 213-793-11-25-47
Email: [email protected]
Received Date: May 22, 2008; Accepted Date: June 15, 2008; Published Date: June 19, 2008
Citation: Abdelouahab C, Abderrahmane B (2008) Comparative Study of the Efficiency of Three Protein-Ligand Docking Programs. J Proteomics Bioinform 1:161-165. doi: 10.4172/jpb.1000022
Copyright: © 2008 Abdelouahab C, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Structure-based lead optimization approaches are increasingly playing a role in the drug-discovery process. Virtual screening by molecular docking has become a largely used approach to lead discovery in the pharmaceutical industry when a high-resolution structure of the biological target of interest is available. The performance of three docking programs (Arguslab, Autodock and FlexX), for virtual database screening, is studied. Autodock and FlexX are well established commercial packages while Arguslab is distributed freely for Windows platforms by Planaria Software. Comparisons of these docking programs and scoring functions using a large and diverse data set of pharmaceutically interesting targets and active compounds are carried out. We focus on the problem of docking and scoring flexible compounds which are sterically capable of docking into a rigid conformation of the receptor. The three dimensional structures of a carefully chosen set of 126 pharmaceutically relevant proteinligand complexes were used for the comparative study. The Autodock methodology is shown to consistently yield enrichments superior to the two alternative methods, while FlexX outperforms largely Arguslab.