Affiliations: Department of Molecular Medicine, Rajiv Gandhi Centre
for Biotechnology, Thiruvananthapuram, Kerala, India
Note: [] Corresponding author: Department of Molecular Medicine, Rajiv
Gandhi Centre for Biotechnology Thycaud. P.O, Thiruvananthapuram- 695 014
Kerala State, India. Tel.: +91 (0) 471 2347973; Fax: +91 (0) 471 2349303;
E-mail: mrpillai@vsnl.com
Abstract: Molecular docking and virtual screening based on molecular docking
have become an integral part of many modern structure-based drug discovery
efforts. Hence, it becomes a useful endeavor to evaluate existing docking
programs, which can assist in the choice of the most suitable docking algorithm
for any particular study. The objective of the current study was to evaluate
the ability of ArgusLab 4.0, a relatively new molecular modeling package in
which molecular docking is implemented, to reproduce crystallographic binding
orientations and to compare its accuracy with that of a well established
commercial package, GOLD. The study also aimed to evaluate the effect of the
nature of the binding site and ligand properties on docking accuracy. The three
dimensional structures of a carefully chosen set of 75 pharmaceutically
relevant protein-ligand complexes were used for the comparative study. The
study revealed that the commercial package outperforms the freely available
docking engine in almost all the parameters tested. However, the study also
revealed that although lagging behind in accuracy, results from ArgusLab are
biologically meaningful. This taken together with the fact that ArgusLab has an
easy to use graphical user interface, means that it can be employed as an
effective teaching tool to demonstrate molecular docking to beginners in this
area.
