Docking Efficiency Comparison of Surflex, a Commercial Package and Arguslab, a Licensable Freewar

Abstract

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 pharmaceu- tical 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 recog- nized 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 pharmaceu- tically 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.