Task-parallel message passing interface implementation of Autodock4 for docking of very large databases of compounds using high-performance super-computers

A message passing interface (MPI)‐based implementation (Autodock4.lga.MPI) of the grid‐based docking program Autodock4 has been developed to allow simultaneous and independent docking of multiple compounds on up to thousands of central processing units (CPUs) using the Lamarkian genetic algorithm. T...

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Bibliographic Details
Published in:Journal of computational chemistry Vol. 32; no. 6; pp. 1202 - 1209
Main Authors: Collignon, Barbara, Schulz, Roland, Smith, Jeremy C., Baudry, Jerome
Format: Journal Article
Language:English
Published: Hoboken Wiley Subscription Services, Inc., A Wiley Company 30.04.2011
Wiley Subscription Services, Inc
Subjects:
Algorithms
Analytical chemistry
automated molecular docking
BASIC BIOLOGICAL SCIENCES
Chemical compounds
COMPUTER CODES
Computer Simulation
Computers
Databases, Protein
Drug Design
GENERAL AND MISCELLANEOUS//MATHEMATICS, COMPUTING, AND INFORMATION SCIENCE
Genetic algorithms
GENETICS
High-Throughput Screening Assays - methods
IMPLEMENTATION
INTERFACES
LIGANDS
MODIFICATIONS
Molecular chemistry
Molecules
MPI parallelization
PROCESSING
PROTEINS
Proteins - chemistry
Software
super-computer
SUPERCOMPUTERS
virtual high-throughput screening
ISSN:0192-8651, 1096-987X, 1096-987X
Online Access:Get full text
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Summary:A message passing interface (MPI)‐based implementation (Autodock4.lga.MPI) of the grid‐based docking program Autodock4 has been developed to allow simultaneous and independent docking of multiple compounds on up to thousands of central processing units (CPUs) using the Lamarkian genetic algorithm. The MPI version reads a single binary file containing precalculated grids that represent the protein–ligand interactions, i.e., van der Waals, electrostatic, and desolvation potentials, and needs only two input parameter files for the entire docking run. In comparison, the serial version of Autodock4 reads ASCII grid files and requires one parameter file per compound. The modifications performed result in significantly reduced input/output activity compared with the serial version. Autodock4.lga.MPI scales up to 8192 CPUs with a maximal overhead of 16.3%, of which two thirds is due to input/output operations and one third originates from MPI operations. The optimal docking strategy, which minimizes docking CPU time without lowering the quality of the database enrichments, comprises the docking of ligands preordered from the most to the least flexible and the assignment of the number of energy evaluations as a function of the number of rotatable bounds. In 24 h, on 8192 high‐performance computing CPUs, the present MPI version would allow docking to a rigid protein of about 300K small flexible compounds or 11 million rigid compounds. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011
Bibliography:National Science Foundation through TeraGrid resources provided by NCSA (Abe) and NICS (Kraken) - No. TG-MCA08X032
ark:/67375/WNG-VT4G2TDW-N
ArticleID:JCC21696
istex:AE5992035D79BFD99924A912E68BB83383953824
Department of Energy Laboratory Directed Research and Development Award in Systems Biology to ORNL
National Energy Research Scientific Computing Center - No. m906
University of Tennessee, the Department of Energy and the UT/ORNL Genome Sciences and Technology graduate program
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USDOE Laboratory Directed Research and Development (LDRD) Program
DE-AC05-00OR22725
ISSN:0192-8651
1096-987X
1096-987X
DOI:10.1002/jcc.21696