DOVIS: an implementation for high-throughput virtual screening using AutoDock

Background: Molecular-docking-based virtual screening is an important tool in drug discovery that is used to significantly reduce the number of possible chemical compounds to be investigated. In addition to the selection of a sound docking strategy with appropriate scoring functions, another technical challenge is to in silico screen millions of compounds in a reasonable time. To meet this challenge, it is necessary to use high performance computing (HPC) platforms and techniques. However, the development of an integrated HPC system that makes efficient use of its elements is not trivial. Results: We have developed an application termed DOVIS that uses AutoDock (version 3) as the docking engine and runs in parallel on a Linux cluster. DOVIS can efficiently dock large numbers (millions) of small molecules (ligands) to a receptor, screening 500 to 1,000 compounds per processor per day. Furthermore, in DOVIS, the docking session is fully integrated and automated in that the inputs are sp...

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Shuxing Zhang, Kamal Kumar, Xiaohui Jiang, Anders Wallqvist, Jaques Reifman
• Keywords: BMCBI 2008, Drug Discovery, Linux Cluster, Virtual Screening