Docking Efficiency Comparison of Surflex, a Commercial Package and Arguslab, a Licensable Freeware
Abdelouahab Chikhi* and Abderrahmane Bensegueni
Laboratory of Theoretical Chemistry, Department of Chemistry. Faculty of Sciences, Mentouri University, Constantine, Algeria
- *Corresponding Author:
- Dr. Abdelouahab Chikhi
Phone : + 213-793-112-547
Email : [email protected]
Received Date: September 06, 2008; Accepted Date: December 20, 2008; Published Date: December 26, 2008
Citation: Abdelouahab C, Abderrahmane B (2008) Docking Efficiency Comparison of Surflex, a Commercial Package and Arguslab, a Licensable Freewar. J Comput Sci Syst Biol 1:081-086. doi: 10.4172/jcsb.1000007
Copyright: © 2008 Abdelouahab C, etal. 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 two docking programs (Arguslab and Surflex), for virtual database screening, is studied. Surflex is well recognized commercial package 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 300 pharmaceutically relevant protein-ligand complexes were used for the comparative study. The results show that Surflex outperforms largely Arguslab in all tests studied.