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VinaMPI: Facilitating multiple receptor high-throughput virtual docking on high-performance computers
Article first published online: 29 JUN 2013
Copyright © 2013 Wiley Periodicals, Inc.
Journal of Computational Chemistry
Volume 34, Issue 25, pages 2212–2221, 30 September 2013
How to Cite
How to cite this article: J. Comput. Chem. 2013, 34, 2212–2221. DOI: 10.1002/jcc.23367, , .
- Issue published online: 19 AUG 2013
- Article first published online: 29 JUN 2013
- Manuscript Accepted: 31 MAY 2013
- Manuscript Revised: 27 MAY 2013
- Manuscript Received: 12 APR 2013
- National Institute for Computational Science (NICS) . Grant Number: TG-MCA08X032
- NIH . Grant Number: 1KL2RR031974
- drug discovery;
- high-throughput docking;
- multiprotein docking;
- high-performance computing
The program VinaMPI has been developed to enable massively large virtual drug screens on leadership-class computing resources, using a large number of cores to decrease the time-to-completion of the screen. VinaMPI is a massively parallel Message Passing Interface (MPI) program based on the multithreaded virtual docking program AutodockVina, and is used to distribute tasks while multithreading is used to speed-up individual docking tasks. VinaMPI uses a distribution scheme in which tasks are evenly distributed to the workers based on the complexity of each task, as defined by the number of rotatable bonds in each chemical compound investigated. VinaMPI efficiently handles multiple proteins in a ligand screen, allowing for high-throughput inverse docking that presents new opportunities for improving the efficiency of the drug discovery pipeline. VinaMPI successfully ran on 84,672 cores with a continual decrease in job completion time with increasing core count. The ratio of the number of tasks in a screening to the number of workers should be at least around 100 in order to have a good load balance and an optimal job completion time. The code is freely available and downloadable. Instructions for downloading and using the code are provided in the Supporting Information. © 2013 Wiley Periodicals, Inc.