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 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.

An In Silico Approach towards the Prediction of Druglikeness Properties of Inhibitors of Plasminogen Activator Inhibitor1

“…Docking calculations were carried out using interactive molecular graphics programs ArgusLab [ 11 ] and PatchDock [ 12 ]. Ligand was placed on a search point in the binding site which was calculated by DEPTH server; a set of diverse and energetically favorable rotations was created.…”

In Silico Docking of HNF-1a Receptor Ligands

“…We performed in silico studies using HNF-1a protein (PDB id: 2GYP·pdb) and fatty acids (listed in the table) by using the software: ISIS/Draw 2.5 [7], ARGUSLAB4.0.1, HEX5.1 [8]. …”

“…ArgusLab is a freely distributed software for Windows platform, commonly used as an introductory molecular modeling package especially in the academic environment [8]. It has a user-friendly interface and an intuitive calculation menus.…”

“…The docking engine approximates an exhaustive search method. It requires a PDB format file for both ligand and receptor [8]. 2D depictions of prospective ligands were drawn using the ISIS/Draw 2.5 and these structures were optimized for energy using AGRUS Lab.…”

Matrix metalloproteinase9 as the protein target in anti-breast cancer drug discovery: an approach by targeting hemopexin domain

“…The software could be free, e.g. AutoDock [92], PLANTS [93] and ArgusLab [94], or bought under a purchased licence such as GOLD [95], Glide [96] and Flexx [97]. The bioinformatics data such as the protein crystal structure, either in apo-form or holoform, is freely downloadable from protein databases such as the Protein Data Bank, commonly abbreviated as PDB (accessible at www.rscb.org).…”