{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,9]],"date-time":"2026-01-09T12:43:28Z","timestamp":1767962608506,"version":"3.49.0"},"reference-count":57,"publisher":"Wiley","issue":"11","license":[{"start":{"date-parts":[[2013,1,23]],"date-time":"2013-01-23T00:00:00Z","timestamp":1358899200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/linproxy.fan.workers.dev:443\/http\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J Comput Chem"],"published-print":{"date-parts":[[2013,4,30]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>A mixed parallel scheme that combines message passing interface (MPI) and multithreading was implemented in the AutoDock Vina molecular docking program. The resulting program, named VinaLC, was tested on the petascale high performance computing (HPC) machines at Lawrence Livermore National Laboratory. To exploit the typical cluster\u2010type supercomputers, thousands of docking calculations were dispatched by the master process to run simultaneously on thousands of slave processes, where each docking calculation takes one slave process on one node, and within the node each docking calculation runs via multithreading on multiple CPU cores and shared memory. Input and output of the program and the data handling within the program were carefully designed to deal with large databases and ultimately achieve HPC on a large number of CPU cores. Parallel performance analysis of the VinaLC program shows that the code scales up to more than 15K CPUs with a very low overhead cost of 3.94%. One million flexible compound docking calculations took only 1.4 h to finish on about 15K CPUs. The docking accuracy of VinaLC has been validated against the DUD data set by the re\u2010docking of X\u2010ray ligands and an enrichment study, 64.4% of the top scoring poses have RMSD values under 2.0 \u00c5. The program has been demonstrated to have good enrichment performance on 70% of the targets in the DUD data set. An analysis of the enrichment factors calculated at various percentages of the screening database indicates VinaLC has very good early recovery of actives. \u00a9 2013 Wiley Periodicals, Inc.<\/jats:p>","DOI":"10.1002\/jcc.23214","type":"journal-article","created":{"date-parts":[[2013,1,23]],"date-time":"2013-01-23T12:08:58Z","timestamp":1358942938000},"page":"915-927","source":"Crossref","is-referenced-by-count":68,"title":["Message passing interface and multithreading hybrid for parallel molecular docking of large databases on petascale high performance computing machines"],"prefix":"10.1002","volume":"34","author":[{"given":"Xiaohua","family":"Zhang","sequence":"first","affiliation":[]},{"given":"Sergio E.","family":"Wong","sequence":"additional","affiliation":[]},{"given":"Felice C.","family":"Lightstone","sequence":"additional","affiliation":[]}],"member":"311","published-online":{"date-parts":[[2013,1,23]]},"reference":[{"key":"e_1_2_6_1_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.1096361"},{"key":"e_1_2_6_2_2","doi-asserted-by":"publisher","DOI":"10.1038\/nrd1549"},{"key":"e_1_2_6_3_2","doi-asserted-by":"publisher","DOI":"10.1208\/s12248-012-9322-0"},{"key":"e_1_2_6_4_2","doi-asserted-by":"publisher","DOI":"10.1038\/nrd892"},{"key":"e_1_2_6_5_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/28.1.235"},{"key":"e_1_2_6_6_2","doi-asserted-by":"publisher","DOI":"10.1038\/432823a"},{"key":"e_1_2_6_7_2","doi-asserted-by":"publisher","DOI":"10.1021\/ci049714"},{"key":"e_1_2_6_8_2","doi-asserted-by":"publisher","DOI":"10.1002\/prot.10115"},{"key":"e_1_2_6_9_2","doi-asserted-by":"publisher","DOI":"10.1021\/jm050362n"},{"key":"e_1_2_6_10_2","doi-asserted-by":"publisher","DOI":"10.1021\/jm0203783"},{"key":"e_1_2_6_11_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.drudis.2007.07.006"},{"key":"e_1_2_6_12_2","doi-asserted-by":"publisher","DOI":"10.1023\/A:1011115820450"},{"key":"e_1_2_6_13_2","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.540130412"},{"key":"e_1_2_6_14_2","doi-asserted-by":"publisher","DOI":"10.1002\/(SICI)1099-1352(199601)9:1<1::AID-JMR241>3.0.CO;2-6"},{"key":"e_1_2_6_15_2","doi-asserted-by":"publisher","DOI":"10.1002\/(SICI)1096-987X(19981115)19:14<1639::AID-JCC10>3.0.CO;2-B"},{"key":"e_1_2_6_16_2","doi-asserted-by":"publisher","DOI":"10.1006\/jmbi.1996.0477"},{"key":"e_1_2_6_17_2","doi-asserted-by":"publisher","DOI":"10.1021\/jm0306430"},{"key":"e_1_2_6_18_2","doi-asserted-by":"publisher","DOI":"10.1021\/jm030644s"},{"key":"e_1_2_6_19_2","doi-asserted-by":"publisher","DOI":"10.1006\/jmbi.1996.0897"},{"key":"e_1_2_6_20_2","unstructured":"PBS Professional home page https:\/\/linproxy.fan.workers.dev:443\/http\/www.pbsworks.com\/."},{"key":"e_1_2_6_21_2","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.21256"},{"key":"e_1_2_6_22_2","first-page":"2","volume":"18","author":"Jiang X. H.","year":"2008","journal-title":"Chem. Cent. J."},{"key":"e_1_2_6_23_2","doi-asserted-by":"publisher","DOI":"10.2174\/138620711797537085"},{"key":"e_1_2_6_24_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkq503"},{"key":"e_1_2_6_25_2","doi-asserted-by":"publisher","DOI":"10.1021\/ci100459b"},{"key":"e_1_2_6_26_2","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-4419-5913-3_56"},{"key":"e_1_2_6_27_2","doi-asserted-by":"publisher","DOI":"10.1261\/rna.1563609"},{"key":"e_1_2_6_28_2","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.20035"},{"key":"e_1_2_6_29_2","unstructured":"CUDA\u2122 is a parallel computing platform and programming model invented by NVIDIA https:\/\/linproxy.fan.workers.dev:443\/http\/www.nvidia.com\/object\/cuda_home_new.html."},{"key":"e_1_2_6_30_2","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.21696"},{"key":"e_1_2_6_31_2","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.21334"},{"key":"e_1_2_6_32_2","doi-asserted-by":"publisher","DOI":"10.1007\/s10822-010-9352-6"},{"key":"e_1_2_6_33_2","doi-asserted-by":"publisher","DOI":"10.1021\/bi101517e"},{"key":"e_1_2_6_34_2","doi-asserted-by":"publisher","DOI":"10.1021\/jm101336m"},{"key":"e_1_2_6_35_2","doi-asserted-by":"publisher","DOI":"10.1021\/ja102100h"},{"key":"e_1_2_6_36_2","first-page":"5","volume":"11955","author":"Chang M. W.","year":"2010","journal-title":"PLoS One"},{"key":"e_1_2_6_37_2","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.540150503"},{"key":"e_1_2_6_38_2","doi-asserted-by":"publisher","DOI":"10.1021\/jm0608356"},{"key":"e_1_2_6_39_2","unstructured":"Boost Organization. Boost C++ Libraries https:\/\/linproxy.fan.workers.dev:443\/http\/www.boost.org\/."},{"key":"e_1_2_6_40_2","doi-asserted-by":"publisher","DOI":"10.1007\/s10822-007-9167-2"},{"key":"e_1_2_6_41_2","doi-asserted-by":"publisher","DOI":"10.1021\/ci900056c"},{"key":"e_1_2_6_42_2","doi-asserted-by":"publisher","DOI":"10.1021\/ci800303k"},{"key":"e_1_2_6_43_2","unstructured":"DUD database A Directory of Useful Decoys Ligand decoy and target structures https:\/\/linproxy.fan.workers.dev:443\/http\/dud.docking.org\/."},{"key":"e_1_2_6_44_2","first-page":"57","volume":"17","author":"Sanner M. F.","year":"1999","journal-title":"J. Mol. Graph. Model."},{"key":"e_1_2_6_45_2","doi-asserted-by":"publisher","DOI":"10.1021\/jm000375v"},{"key":"e_1_2_6_46_2","unstructured":"SLURM. Simple Linux Utility for Resource Management https:\/\/linproxy.fan.workers.dev:443\/https\/computing.llnl.gov\/linux\/slurm\/."},{"key":"e_1_2_6_47_2","unstructured":"Sequoia the new IBM 20\u2010petaflops supercomputing system at LLNL https:\/\/linproxy.fan.workers.dev:443\/https\/asc.llnl.gov\/computing_resources\/sequoia\/."},{"key":"e_1_2_6_48_2","unstructured":"InfiniBand is a switched fabric communications link used in high\u2010performance computing and enterprise data centers https:\/\/linproxy.fan.workers.dev:443\/http\/www.infinibandta.org\/."},{"key":"e_1_2_6_49_2","unstructured":"MVAPICH: MPI over InfiniBand 10GigE\/iWARP and RoCE https:\/\/linproxy.fan.workers.dev:443\/http\/mvapich.cse.ohio\u2010state.edu\/."},{"key":"e_1_2_6_50_2","unstructured":"mpiP: Lightweight Scalable MPI Profiling https:\/\/linproxy.fan.workers.dev:443\/http\/mpip.sourceforge.net\/."},{"key":"e_1_2_6_51_2","unstructured":"Open|SpeedShop an open source multi platform Linux performance tool https:\/\/linproxy.fan.workers.dev:443\/http\/www.openspeedshop.org."},{"key":"e_1_2_6_52_2","doi-asserted-by":"publisher","DOI":"10.1038\/scientificamerican1000-82"},{"key":"e_1_2_6_53_2","doi-asserted-by":"publisher","DOI":"10.1021\/ci800023x"},{"key":"e_1_2_6_54_2","doi-asserted-by":"publisher","DOI":"10.1023\/A:1008100132405"},{"key":"e_1_2_6_55_2","doi-asserted-by":"publisher","DOI":"10.1002\/prot.10296"},{"key":"e_1_2_6_56_2","doi-asserted-by":"publisher","DOI":"10.1021\/jm020406h"},{"key":"e_1_2_6_57_2","doi-asserted-by":"publisher","DOI":"10.1007\/s10822-007-9114-2"}],"container-title":["Journal of Computational Chemistry"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/linproxy.fan.workers.dev:443\/https\/api.wiley.com\/onlinelibrary\/tdm\/v1\/articles\/10.1002%2Fjcc.23214","content-type":"unspecified","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/linproxy.fan.workers.dev:443\/https\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/jcc.23214","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,10,9]],"date-time":"2023-10-09T19:06:54Z","timestamp":1696878414000},"score":1,"resource":{"primary":{"URL":"https:\/\/linproxy.fan.workers.dev:443\/https\/onlinelibrary.wiley.com\/doi\/10.1002\/jcc.23214"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,1,23]]},"references-count":57,"journal-issue":{"issue":"11","published-print":{"date-parts":[[2013,4,30]]}},"alternative-id":["10.1002\/jcc.23214"],"URL":"https:\/\/linproxy.fan.workers.dev:443\/https\/doi.org\/10.1002\/jcc.23214","archive":["Portico"],"relation":{},"ISSN":["0192-8651","1096-987X"],"issn-type":[{"value":"0192-8651","type":"print"},{"value":"1096-987X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2013,1,23]]}}}