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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Vydané v:	Journal of computational chemistry Ročník 32; číslo 6; s. 1202 - 1209
Hlavní autori:	Collignon, Barbara, Schulz, Roland, Smith, Jeremy C., Baudry, Jerome
Médium:	Journal Article
Jazyk:	English
Vydavateľské údaje:	Hoboken Wiley Subscription Services, Inc., A Wiley Company 30.04.2011 Wiley Subscription Services, Inc
Predmet:	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
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Abstract	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
AbstractList	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. [PUBLICATION ABSTRACT] 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. 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 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.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.
Author	Collignon, Barbara Schulz, Roland Baudry, Jerome Smith, Jeremy C.
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BackLink	https://www.ncbi.nlm.nih.gov/pubmed/21387347$$D View this record in MEDLINE/PubMed https://www.osti.gov/biblio/1037144$$D View this record in Osti.gov
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Cites_doi	10.1021/jm901191q 10.1007/s10822-005-8483-7 10.1021/jm901386e 10.1002/1521-3773(20020802)41:15<2644::AID-ANIE2644>3.0.CO;2-O 10.1186/1752-153X-2-18 10.1002/(SICI)1096-987X(19981115)19:14<1639::AID-JCC10>3.0.CO;2-B 10.1107/S0021889807011053 10.1021/ci7000346 10.1021/ja902302h 10.1002/jcc.21334 10.1016/0022-2836(82)90153-X 10.1021/jm060999m 10.1093/nar/28.1.235 10.1021/ci7000378 10.1021/jm800726b 10.1093/protein/6.7.723 10.1021/jm0608356 10.1007/s10822-006-9060-4 10.1021/ci900186w 10.1021/jm8001197 10.1093/bioinformatics/btq149 10.1002/jcc.540130412 10.1021/ed082p890
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Snippet	A message passing interface (MPI)‐based implementation (Autodock4.lga.MPI) of the grid‐based docking program Autodock4 has been developed to allow simultaneous... A message passing interface (MPI)-based implementation (Autodock4.lga.MPI) of the grid-based docking program Autodock4 has been developed to allow simultaneous...
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SubjectTerms	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
Title	Task-parallel message passing interface implementation of Autodock4 for docking of very large databases of compounds using high-performance super-computers
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Volume	32
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