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Title: Accelerating virtual high-throughput ligand docking: current technology and case study on a petascale supercomputer: ACCELERATING VIRTUAL HIGH-THROUGHPUT LIGAND DOCKING

Abstract

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.

Authors:
 [1];  [2];  [2];  [1];  [1]
  1. Univ. of Tennessee, Knoxville, TN (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
  2. Georgetown Univ. Medical Center, Washington, DC (United States). Lombardi Comprehensive Cancer Center
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Oak Ridge Leadership Computing Facility (OLCF)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1565107
Resource Type:
Accepted Manuscript
Journal Name:
Concurrency and Computation. Practice and Experience
Additional Journal Information:
Journal Volume: 26; Journal Issue: 6; Journal ID: ISSN 1532-0626
Publisher:
Wiley
Country of Publication:
United States
Language:
English
Subject:
97 MATHEMATICS AND COMPUTING; Computer Science

Citation Formats

Ellingson, Sally R., Dakshanamurthy, Sivanesan, Brown, Milton, Smith, Jeremy C., and Baudry, Jerome. Accelerating virtual high-throughput ligand docking: current technology and case study on a petascale supercomputer: ACCELERATING VIRTUAL HIGH-THROUGHPUT LIGAND DOCKING. United States: N. p., 2013. Web. doi:10.1002/cpe.3070.
Ellingson, Sally R., Dakshanamurthy, Sivanesan, Brown, Milton, Smith, Jeremy C., & Baudry, Jerome. Accelerating virtual high-throughput ligand docking: current technology and case study on a petascale supercomputer: ACCELERATING VIRTUAL HIGH-THROUGHPUT LIGAND DOCKING. United States. doi:10.1002/cpe.3070.
Ellingson, Sally R., Dakshanamurthy, Sivanesan, Brown, Milton, Smith, Jeremy C., and Baudry, Jerome. Thu . "Accelerating virtual high-throughput ligand docking: current technology and case study on a petascale supercomputer: ACCELERATING VIRTUAL HIGH-THROUGHPUT LIGAND DOCKING". United States. doi:10.1002/cpe.3070. https://www.osti.gov/servlets/purl/1565107.
@article{osti_1565107,
title = {Accelerating virtual high-throughput ligand docking: current technology and case study on a petascale supercomputer: ACCELERATING VIRTUAL HIGH-THROUGHPUT LIGAND DOCKING},
author = {Ellingson, Sally R. and Dakshanamurthy, Sivanesan and Brown, Milton and Smith, Jeremy C. and Baudry, Jerome},
abstractNote = {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.},
doi = {10.1002/cpe.3070},
journal = {Concurrency and Computation. Practice and Experience},
number = 6,
volume = 26,
place = {United States},
year = {2013},
month = {6}
}

Journal Article:
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