Accelerating virtual high-throughput ligand docking: current technology and case study on a petascale supercomputer

Ellingson, Sally R.; Dakshanamurthy, Sivanesan; Brown, Milton; Smith, Jeremy C.; Baudry, Jerome

doi:10.1002/cpe.3070

Accelerating virtual high-throughput ligand docking: current technology and case study on a petascale supercomputer

Journal Article · Thu Jun 20 00:00:00 EDT 2013 · Concurrency and Computation. Practice and Experience

DOI:https://doi.org/10.1002/cpe.3070· OSTI ID:1565107

Ellingson, Sally R. ^[1]; Dakshanamurthy, Sivanesan ^[2]; Brown, Milton ^[2]; Smith, Jeremy C. ^[1]; Baudry, Jerome ^[1]

Univ. of Tennessee, Knoxville, TN (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Georgetown Univ. Medical Center, Washington, DC (United States). Lombardi Comprehensive Cancer Center

In this paper, we give the current state of high-throughput virtual screening. We describe a case study of using a task-parallel Message Passing Interface version of AutoDock4 to run a virtual high-throughput screen of one million compounds on the Jaguar Cray XK6 Supercomputer at Oak Ridge National Laboratory. We include a description of scripts developed to increase the efficiency of the predocking file preparation and postdocking analysis. A detailed tutorial, scripts, and source code for this Message Passing Interface version of AutoDock4 are available online at http://www.bio.utk.edu/baudrylab/autodockmpi.htm.

View Accepted Manuscript (DOE)

Research Organization:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States). Oak Ridge Leadership Computing Facility (OLCF)

Sponsoring Organization:: USDOE Office of Science (SC)

OSTI ID:: 1565107

Journal Information:: Concurrency and Computation. Practice and Experience, Journal Name: Concurrency and Computation. Practice and Experience Journal Issue: 6 Vol. 26; ISSN 1532-0626

Publisher:: WileyCopyright Statement

Country of Publication:: United States

Language:: English

References (18)

Task-parallel message passing interface implementation of Autodock4 for docking of very large databases of compounds using high-performance super-computers Collignon, Barbara; Schulz, Roland; Smith, Jeremy C. Journal of Computational Chemistry, Vol. 32, Issue 6 https://doi.org/10.1002/jcc.21696	journal	December 2010
A survey of computational molecular science using graphics processing units: Survey of computational molecular science on GPUs Harvey, M. J.; De Fabritiis, Gianni Wiley Interdisciplinary Reviews: Computational Molecular Science, Vol. 2, Issue 5 https://doi.org/10.1002/wcms.1101	journal	April 2012
Prediction of potential toxicity and side effect protein targets of a small molecule by a ligand–protein inverse docking approach Chen, Y. Z.; Ung, C. Y. Journal of Molecular Graphics and Modelling, Vol. 20, Issue 3 https://doi.org/10.1016/S1093-3263(01)00109-7	journal	January 2001
Structural modelling and dynamics of proteins for insights into drug interactions Werner, Tim; Morris, Michael B.; Dastmalchi, Siavoush Advanced Drug Delivery Reviews, Vol. 64, Issue 4 https://doi.org/10.1016/j.addr.2011.11.011	journal	March 2012
Evaluation of various inverse docking schemes in multiple targets identification Hui-fang, Liu; Qing, Shen; Jian, Zhang Journal of Molecular Graphics and Modelling, Vol. 29, Issue 3 https://doi.org/10.1016/j.jmgm.2010.09.004	journal	November 2010
Virtual screening on large scale grids Jacq, Nicolas; Breton, Vincent; Chen, Hsin-Yen Parallel Computing, Vol. 33, Issue 4-5 https://doi.org/10.1016/j.parco.2007.02.010	journal	May 2007
ZINC: A Free Tool to Discover Chemistry for Biology Irwin, John J.; Sterling, Teague; Mysinger, Michael M. Journal of Chemical Information and Modeling, Vol. 52, Issue 7 https://doi.org/10.1021/ci3001277	journal	June 2012
Ensemble-Based Virtual Screening Reveals Potential Novel Antiviral Compounds for Avian Influenza Neuraminidase Cheng, Lily S.; Amaro, Rommie E.; Xu, Dong Journal of Medicinal Chemistry, Vol. 51, Issue 13 https://doi.org/10.1021/jm8001197	journal	July 2008
Virtual screening of chemical libraries Shoichet, Brian K. Nature, Vol. 432, Issue 7019 https://doi.org/10.1038/nature03197	journal	December 2004
e-Science Infrastructure Integration Invariants to Enable HTC and HPC Interoperability Applications Riedel, M.; Memon, M. S.; Memon, A. S. Distributed Processing, Workshops and Phd Forum (IPDPSW), 2011 IEEE International Symposium on Parallel and Distributed Processing Workshops and Phd Forum https://doi.org/10.1109/IPDPS.2011.238	conference	May 2011
Many-task computing for grids and supercomputers Raicu, Ioan; Foster, Ian T. 2008 Workshop on Many-Task Computing on Grids and Supercomputers (MTAGS) https://doi.org/10.1109/MTAGS.2008.4777912	conference	November 2008
Parallelization of Virtual Screening in Drug Discovery on Massively Parallel Architectures Guerrero, Gines D.; Perez-S´nchez, Horacio E.; Cecilia, Jose M. 2012 20th Euromicro International Conference on Parallel, Distributed and Network-Based Processing (PDP 2012) https://doi.org/10.1109/PDP.2012.26	conference	February 2012
Toward loosely coupled programming on petascale systems Raicu, Ioan; Wilde, Mike 2008 SC - International Conference for High Performance Computing, Networking, Storage and Analysis https://doi.org/10.1109/SC.2008.5219768	conference	November 2008
Grid-Enabled High-Throughput In Silico Screening Against Influenza A Neuraminidase Lee, Hurng-Chun; Salzemann, Jean; Jacq, Nicolas IEEE Transactions on Nanobioscience, Vol. 5, Issue 4 https://doi.org/10.1109/TNB.2006.887943	journal	January 2006
High-throughput virtual molecular docking: Hadoop implementation of AutoDock4 on a private cloud Ellingson, Sally R.; Baudry, Jerome Proceedings of the second international workshop on Emerging computational methods for the life sciences - ECMLS '11 https://doi.org/10.1145/1996023.1996028	conference	January 2011
Accelerating multiple target drug screening on GPUs Sánchez-Linares, Irene; Pérez-Sánchez, Horacio; Guerrero, Ginés D. Proceedings of the 9th International Conference on Computational Methods in Systems Biology - CMSB '11 https://doi.org/10.1145/2037509.2037523	conference	January 2011
Calculation of Protein-Ligand Binding Affinities Gilson, Michael K.; Zhou, Huan-Xiang Annual Review of Biophysics and Biomolecular Structure, Vol. 36, Issue 1 https://doi.org/10.1146/annurev.biophys.36.040306.132550	journal	June 2007
Accessible High-Throughput Virtual Screening Molecular Docking Software for Students and Educators Jacob, Reed B.; Andersen, Tim; McDougal, Owen M. PLoS Computational Biology, Vol. 8, Issue 5 https://doi.org/10.1371/journal.pcbi.1002499	journal	May 2012

Cited By (1)

1001 Ways to run AutoDock Vina for virtual screening Jaghoori, Mohammad Mahdi; Bleijlevens, Boris; Olabarriaga, Silvia D. Journal of Computer-Aided Molecular Design, Vol. 30, Issue 3 https://doi.org/10.1007/s10822-016-9900-9	journal	February 2016

Similar Records

VinaMPI: Facilitating multiple receptor high-throughput virtual docking on high-performance computers

Journal Article · Mon Sep 30 00:00:00 EDT 2013 · Journal of Computational Chemistry · OSTI ID:1265934

An analysis of computational workloads for the ORNL Jaguar system. In: ICS '12 Proceedings of the 26th ACM international conference on Supercomputing

Conference · Sat Dec 31 23:00:00 EST 2011 · OSTI ID:1567624

Supercomputer throughput benchmarks for the CRAY-1S and CYBER 205 with estimates for class VII supercomputers

Journal Article · Sat Dec 31 23:00:00 EST 1988 · International Journal of Supercomputer Application; (USA) · OSTI ID:5437194

Related Subjects

97 MATHEMATICS AND COMPUTING
Computer Science

Accelerating virtual high-throughput ligand docking: current technology and case study on a petascale supercomputer

Citation Formats

References (18)

Cited By (1)

Similar Records

Related Subjects