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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Vydáno v:	Journal of computational chemistry Ročník 32; číslo 6; s. 1202 - 1209
Hlavní autoři:	Collignon, Barbara, Schulz, Roland, Smith, Jeremy C., Baudry, Jerome
Médium:	Journal Article
Jazyk:	angličtina
Vydáno:	Hoboken Wiley Subscription Services, Inc., A Wiley Company 30.04.2011 Wiley Subscription Services, Inc
Témata:	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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References	Ravindranathan, K. P.;Mandiyan, V.;Ekkati, A. R.;Bae, J. H.;Schlessinger, J.;Jorgensen, W. L. J Med Chem 2010, 53, 1662. Tame, J. J Comput Aid Mol Design 2005, 19, 445. Meng, E. C.;Shoichet, B. K.;Kuntz, I. D. J Comput Chem 1991, 13, 505. Prakhov, N. D.;Chernorudskiy, A. L.;Gainullin, M. R. Bioinformatics 2010, 26, 1374. Lang, P. T.;Moustakas, D.;Brozell, S.;Carrascal, N.;Mukherjee, S.;Pegg, S.;Raha, K.;Shivakumar, D.;Rizzo, R.;Case, D.;Shoichet, B.;Kuntz, I. DOCK 6.3 Users Manual; University of California: San Francisco, CA, 2010. Trott, O.;Olson, A. J. J Comput Chem 2010, 31, 455. Baudry, J.;Hergenrother, P. J. J Chem Ed 2005, 82, 890. Kuntz, I. D.;Blaney, J. M.;Oatley, S. J.;Langidge, R.;Ferrin, T. E. J Mol Biol 1982, 161, 269. Moustakas, D. T.;Lang, P. T.;Pegg, S.;Pettersen, E.;Kuntz, I. D.;Brooijmans N.;Rizzo, R. C. J Comput Aid Mol Design 2006, 20, 601. Severance, C.;Dowd, K. High Performance Computing, 2nd ed.; O'Reilly Media: Sebastopol, CA, 1998. Huang, N.;Shoichet, B. K.;Irwin, J. J. J Med Chem 2006, 49, 6789. Leach, A. R.;Shoichet, B. K.;Peishoff, C. E. J Med Chem 2006, 49, 5851. Zhou, Z.;Felts, A. K.;Friesner, R. A.;Levy, R. M. J Chem Inf Model 2007, 47, 1599. Shoichet, B. K.;Kuntz, I. D. Prot Eng 1993, 6, 723. Berman, H. M.;Westbrook, J.;Feng, Z.;Gilliland, G.;Bhat, T. N.;Weissig, H.;Shindyalov, I. N.;Bourne, P. E. Nucleic Acid Res 2000, 28, 235. Kova, A.;Konc, J.;Vehar, B.;Bostock, J. M.;Chopra, I.;Janei, D.;Gobec, S. J Med Chem 2008, 51, 7442. Blum, L.;Reymond, J.-L. J Am Chem Soc 2009, 131, 8732. Raicu, I.;Zhang, Z.;Wilde, M.;Foster, I.;Beckman, P.;Iskra, K.;Clifford, B. In Proceedings of High Performance Computing, Networking, Storage and Analysis. Supercomputing Conference. SC 2008. Austin, TX; 2008; pp. 1-12. Morris, G. M.;Goodsell, D. S.;Halliday, R. S.;Huey, R.;Hart, W. E.;Belew, R. K.;Olson., A. J. J Comput Chem 1998, 19, 1639. Khodade, P.;Prabhu, R.;Chandra, N.;Raha, S.;Govindarajan, R. JAppl Crystallogr 2007, 40, 598. Onodera, K.;Satou, K.;Hirota, H. J Chem Inf Model 2007, 47, 1609. Chiu, T. L.;Solberg, J.;Patil, S.;Geders, T. W.;Zhang, X.;Rangarajan, S.;Francis, R.;Finzel, B. C.;Walters, M. A.;Hook, D. J.;Amin, E. A. J Chem Inf Model 2009, 49, 2726. Cheng, L. S.;Amaro, R. E.;Xu, D.;Li, W. W.;Arzberger, P. W.;McCammon, J. A. J Med Chem 2008, 51, 3878. Jiang, X.;Kumar, K.;Hu, X.;Wallqvist, A.;Reifman, J. Chem Cent J 2008, 2, 18. Gohlke, H.;Klebe, G. Angew Chem Int Ed 2002, 41, 2644. Okamoto, M.;Takayama, K.;Shimizu, T.;Ishida, K.;Takahashi, O.;Furuya, T. J Med Chem 2009, 52, 7323. 2010; 53 2010; 31 2009; 52 2005; 19 1998; 19 2006; 20 2010; 26 2000; 28 2002; 41 1991; 13 2010 2006; 49 1998 2008 1997 2005; 82 2007; 40 2009; 131 2008; 51 2008; 2 2009; 49 2007; 47 1993; 6 1982; 161 Lang P. T. (e_1_2_6_24_2) 2010 e_1_2_6_31_2 Raicu I. (e_1_2_6_17_2) 2008 e_1_2_6_30_2 e_1_2_6_18_2 e_1_2_6_19_2 e_1_2_6_35_2 e_1_2_6_13_2 e_1_2_6_34_2 e_1_2_6_10_2 e_1_2_6_33_2 e_1_2_6_11_2 e_1_2_6_32_2 e_1_2_6_16_2 e_1_2_6_39_2 e_1_2_6_38_2 e_1_2_6_14_2 e_1_2_6_37_2 e_1_2_6_15_2 e_1_2_6_36_2 e_1_2_6_42_2 e_1_2_6_20_2 e_1_2_6_41_2 e_1_2_6_40_2 e_1_2_6_8_2 e_1_2_6_7_2 e_1_2_6_9_2 e_1_2_6_29_2 e_1_2_6_4_2 e_1_2_6_3_2 Severance C. (e_1_2_6_12_2) 1998 e_1_2_6_6_2 e_1_2_6_5_2 e_1_2_6_23_2 e_1_2_6_2_2 e_1_2_6_22_2 e_1_2_6_21_2 e_1_2_6_28_2 e_1_2_6_43_2 e_1_2_6_27_2 e_1_2_6_44_2 e_1_2_6_26_2 e_1_2_6_25_2
References_xml	– reference: Ravindranathan, K. P.;Mandiyan, V.;Ekkati, A. R.;Bae, J. H.;Schlessinger, J.;Jorgensen, W. L. J Med Chem 2010, 53, 1662. – reference: Baudry, J.;Hergenrother, P. J. J Chem Ed 2005, 82, 890. – reference: Severance, C.;Dowd, K. High Performance Computing, 2nd ed.; O'Reilly Media: Sebastopol, CA, 1998. – reference: Trott, O.;Olson, A. J. J Comput Chem 2010, 31, 455. – reference: Kuntz, I. D.;Blaney, J. M.;Oatley, S. J.;Langidge, R.;Ferrin, T. E. J Mol Biol 1982, 161, 269. – reference: Khodade, P.;Prabhu, R.;Chandra, N.;Raha, S.;Govindarajan, R. JAppl Crystallogr 2007, 40, 598. – reference: Onodera, K.;Satou, K.;Hirota, H. J Chem Inf Model 2007, 47, 1609. – reference: Chiu, T. L.;Solberg, J.;Patil, S.;Geders, T. W.;Zhang, X.;Rangarajan, S.;Francis, R.;Finzel, B. C.;Walters, M. A.;Hook, D. J.;Amin, E. A. J Chem Inf Model 2009, 49, 2726. – reference: Moustakas, D. T.;Lang, P. T.;Pegg, S.;Pettersen, E.;Kuntz, I. D.;Brooijmans N.;Rizzo, R. C. J Comput Aid Mol Design 2006, 20, 601. – reference: Berman, H. M.;Westbrook, J.;Feng, Z.;Gilliland, G.;Bhat, T. N.;Weissig, H.;Shindyalov, I. N.;Bourne, P. E. Nucleic Acid Res 2000, 28, 235. – reference: Blum, L.;Reymond, J.-L. J Am Chem Soc 2009, 131, 8732. – reference: Shoichet, B. K.;Kuntz, I. D. Prot Eng 1993, 6, 723. – reference: Morris, G. M.;Goodsell, D. S.;Halliday, R. S.;Huey, R.;Hart, W. E.;Belew, R. K.;Olson., A. J. J Comput Chem 1998, 19, 1639. – reference: Raicu, I.;Zhang, Z.;Wilde, M.;Foster, I.;Beckman, P.;Iskra, K.;Clifford, B. In Proceedings of High Performance Computing, Networking, Storage and Analysis. Supercomputing Conference. SC 2008. Austin, TX; 2008; pp. 1-12. – reference: Meng, E. C.;Shoichet, B. K.;Kuntz, I. D. J Comput Chem 1991, 13, 505. – reference: Prakhov, N. D.;Chernorudskiy, A. L.;Gainullin, M. R. Bioinformatics 2010, 26, 1374. – reference: Huang, N.;Shoichet, B. K.;Irwin, J. J. J Med Chem 2006, 49, 6789. – reference: Gohlke, H.;Klebe, G. Angew Chem Int Ed 2002, 41, 2644. – reference: Leach, A. R.;Shoichet, B. K.;Peishoff, C. E. J Med Chem 2006, 49, 5851. – reference: Jiang, X.;Kumar, K.;Hu, X.;Wallqvist, A.;Reifman, J. Chem Cent J 2008, 2, 18. – reference: Cheng, L. S.;Amaro, R. E.;Xu, D.;Li, W. W.;Arzberger, P. W.;McCammon, J. A. J Med Chem 2008, 51, 3878. – reference: Kova, A.;Konc, J.;Vehar, B.;Bostock, J. M.;Chopra, I.;Janei, D.;Gobec, S. J Med Chem 2008, 51, 7442. – reference: Lang, P. T.;Moustakas, D.;Brozell, S.;Carrascal, N.;Mukherjee, S.;Pegg, S.;Raha, K.;Shivakumar, D.;Rizzo, R.;Case, D.;Shoichet, B.;Kuntz, I. DOCK 6.3 Users Manual; University of California: San Francisco, CA, 2010. – reference: Tame, J. J Comput Aid Mol Design 2005, 19, 445. – reference: Okamoto, M.;Takayama, K.;Shimizu, T.;Ishida, K.;Takahashi, O.;Furuya, T. J Med Chem 2009, 52, 7323. – reference: Zhou, Z.;Felts, A. K.;Friesner, R. A.;Levy, R. M. J Chem Inf Model 2007, 47, 1599. – volume: 28 start-page: 235 year: 2000 publication-title: Nucleic Acid Res – start-page: 1 year: 2008 end-page: 12 – volume: 2 start-page: 18 year: 2008 publication-title: Chem Cent J – volume: 53 start-page: 1662 year: 2010 publication-title: J Med Chem – volume: 51 start-page: 3878 year: 2008 publication-title: J Med Chem – volume: 19 start-page: 1639 year: 1998 publication-title: J Comput Chem – volume: 26 start-page: 1374 year: 2010 publication-title: Bioinformatics – volume: 6 start-page: 723 year: 1993 publication-title: Prot Eng – volume: 51 start-page: 7442 year: 2008 publication-title: J Med Chem – volume: 47 start-page: 1609 year: 2007 publication-title: J Chem Inf Model – volume: 52 start-page: 7323 year: 2009 publication-title: J Med Chem – volume: 41 start-page: 2644 year: 2002 publication-title: Angew Chem Int Ed – year: 1998 – volume: 13 start-page: 505 year: 1991 publication-title: J Comput Chem – year: 2010 – volume: 19 start-page: 445 year: 2005 publication-title: J Comput Aid Mol Design – volume: 49 start-page: 2726 year: 2009 publication-title: J Chem Inf Model – volume: 31 start-page: 455 year: 2010 publication-title: J Comput Chem – volume: 82 start-page: 890 year: 2005 publication-title: J Chem Ed – year: 2008 – volume: 49 start-page: 5851 year: 2006 publication-title: J Med Chem – volume: 131 start-page: 8732 year: 2009 publication-title: J Am Chem Soc – year: 1997 – volume: 47 start-page: 1599 year: 2007 publication-title: J Chem Inf Model – volume: 161 start-page: 269 year: 1982 publication-title: J Mol Biol – volume: 40 start-page: 598 year: 2007 publication-title: JAppl Crystallogr – volume: 20 start-page: 601 year: 2006 publication-title: J Comput Aid Mol Design – volume: 49 start-page: 6789 year: 2006 publication-title: J Med Chem – ident: e_1_2_6_8_2 doi: 10.1021/jm901191q – ident: e_1_2_6_11_2 doi: 10.1007/s10822-005-8483-7 – ident: e_1_2_6_16_2 – ident: e_1_2_6_5_2 doi: 10.1021/jm901386e – ident: e_1_2_6_44_2 – ident: e_1_2_6_27_2 – ident: e_1_2_6_2_2 doi: 10.1002/1521-3773(20020802)41:15<2644::AID-ANIE2644>3.0.CO;2-O – ident: e_1_2_6_32_2 doi: 10.1186/1752-153X-2-18 – ident: e_1_2_6_19_2 doi: 10.1002/(SICI)1096-987X(19981115)19:14<1639::AID-JCC10>3.0.CO;2-B – volume-title: High Performance Computing year: 1998 ident: e_1_2_6_12_2 – ident: e_1_2_6_33_2 doi: 10.1107/S0021889807011053 – start-page: 1 volume-title: Proceedings of High Performance Computing, Networking, Storage and Analysis year: 2008 ident: e_1_2_6_17_2 – ident: e_1_2_6_4_2 doi: 10.1021/ci7000346 – ident: e_1_2_6_14_2 doi: 10.1021/ja902302h – ident: e_1_2_6_35_2 – ident: e_1_2_6_43_2 – ident: e_1_2_6_15_2 – ident: e_1_2_6_38_2 – ident: e_1_2_6_26_2 – ident: e_1_2_6_34_2 doi: 10.1002/jcc.21334 – ident: e_1_2_6_23_2 – ident: e_1_2_6_18_2 – ident: e_1_2_6_22_2 doi: 10.1016/0022-2836(82)90153-X – ident: e_1_2_6_42_2 – ident: e_1_2_6_3_2 doi: 10.1021/jm060999m – ident: e_1_2_6_41_2 doi: 10.1093/nar/28.1.235 – volume-title: DOCK 6.3 Users Manual year: 2010 ident: e_1_2_6_24_2 – ident: e_1_2_6_37_2 – ident: e_1_2_6_28_2 – ident: e_1_2_6_10_2 doi: 10.1021/ci7000378 – ident: e_1_2_6_6_2 doi: 10.1021/jm800726b – ident: e_1_2_6_21_2 doi: 10.1093/protein/6.7.723 – ident: e_1_2_6_40_2 doi: 10.1021/jm0608356 – ident: e_1_2_6_29_2 doi: 10.1007/s10822-006-9060-4 – ident: e_1_2_6_13_2 doi: 10.1021/ci900186w – ident: e_1_2_6_39_2 – ident: e_1_2_6_9_2 doi: 10.1021/jm8001197 – ident: e_1_2_6_31_2 doi: 10.1093/bioinformatics/btq149 – ident: e_1_2_6_30_2 – ident: e_1_2_6_36_2 – ident: e_1_2_6_20_2 doi: 10.1002/jcc.540130412 – ident: e_1_2_6_25_2 – ident: e_1_2_6_7_2 doi: 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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