VsLab - An implementation for virtual high-throughput screening using AutoDock and VMD

摘要

Molecular docking is a key tool in structural molecular biology and computer-assisted drug design. The goal of ligand-protein docking is to predict the predominant binding mode(s) of a ligand with a protein of known three-dimensional structure. There is much docking software that has been successfully used in a myriad of keystone problems; however, as commonly happens with most of the scientific software, the programs are often complex and a deep knowledge is required for the common user to carry out standard steps. This is an obstacle and a cornerstone issue for the research teams in the fields of chemistry and the life sciences, who are interested in conducting this kind of calculations but do not have enough programing skills. To overcome these limitations, we have designed vsLab (virtual screening lab), an easy-to-use graphical interface for the well-known molecular docking software AutoGrid/AutoDock that has been included into VMD as a plug-in. This program allows almost anyone to use AutoDock and AutoGrid for simple docking or for virtual screening campaigns without requiring any deep knowledge about these techniques. The potential associated to this software makes it an attractive choice for more advanced users that can use vsLab to increase workflow and productivity of everyday tasks. The program can be freely obtained at http://www.fc.up.pt/pessoasscerque/vsLab/vLab/HomePage.html