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 specified via a graphical user interface, the calculations are fully integrated with a Linux cluster queuing system for parallel processing, and the results can be visualized and queried.


CONCLUSIONS
DOVIS removes most of the complexities and organizational problems associated with large-scale high-throughput virtual screening, and provides a convenient and efficient solution for AutoDock users to use this software in a Linux cluster platform.
Zhang
Shuxing
S
Biotechnology HPC Software Applications Institute, Telemedicine and Advanced Technology Research Center, US Army Medical Research and Materiel Command, Fort Detrick, MD 21702, USA. shuzhang@mdanderson.org
Kumar
Kamal
K
Jiang
Xiaohui
X
Wallqvist
Anders
A
Reifman
Jaques
J
D001665:Binding Sites; D003198:Computer Simulation; D015195:Drug Design; D008956:Models, Chemical; D004364:Pharmaceutical Preparations / Q000737:chemistry*; D011485:Protein Binding; D011506:Proteins / Q000737:chemistry*; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software; D014584:User-Computer Interface
D004364:Pharmaceutical Preparations; D011506:Proteins