MS-DOCK: Accurate multiple conformation generator and rigid docking protocol for multi-step virtual ligand screening

Background: The number of protein targets with a known or predicted tri-dimensional structure and of drug-like chemical compounds is growing rapidly and so is the need for new therapeutic compounds or chemical probes. Performing flexible structure-based virtual screening computations on thousands of targets with millions of molecules is intractable to most laboratories nor indeed desirable. Since shape complementarity is of primary importance for most proteinligand interactions, we have developed a tool/protocol based on rigid-body docking to select compounds that fit well into binding sites. Results: Here we present an efficient multiple conformation rigid-body docking approach, MSDOCK, which is based on the program DOCK. This approach can be used as the first step of a multi-stage docking/scoring protocol. First, we developed and validated the Multiconf-DOCK tool that generates several conformers per input ligand. Then, each generated conformer (bioactives and 37970 decoys) was dock...

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Nicolas Sauton, David Lagorce, Bruno O. Villoutreix, Maria A. Miteva
• Keywords: BMCBI 2008, Multi-step Structure-based Screening, Rigid-body Docking Approach, Structure-based Virtual Screening