{"id":"https://openalex.org/W2169244518","doi":"https://doi.org/10.1186/1758-2946-3-12","title":"Multilevel Parallelization of AutoDock 4.2","display_name":"Multilevel Parallelization of AutoDock 4.2","publication_year":2011,"publication_date":"2011-04-28","ids":{"openalex":"https://openalex.org/W2169244518","doi":"https://doi.org/10.1186/1758-2946-3-12","mag":"2169244518","pmid":"https://pubmed.ncbi.nlm.nih.gov/21527034"},"language":"en","primary_location":{"id":"doi:10.1186/1758-2946-3-12","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-3-12","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-3-12","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-3-12","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5075917916","display_name":"Andrew P. Norgan","orcid":"https://orcid.org/0000-0002-2955-2066"},"institutions":[{"id":"https://openalex.org/I4210125099","display_name":"Mayo Clinic in Arizona","ror":"https://ror.org/03jp40720","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1330342723","https://openalex.org/I4210125099"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Andrew P Norgan","raw_affiliation_strings":["IBM, Rochester, MN, USA. cpsosa@us.ibm.com","Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"IBM, Rochester, MN, USA. cpsosa@us.ibm.com","institution_ids":[]},{"raw_affiliation_string":"Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA","institution_ids":["https://openalex.org/I4210125099"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005640160","display_name":"Paul Coffman","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Paul K Coffman","raw_affiliation_strings":["IBM, Rochester, MN, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"IBM, Rochester, MN, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110176668","display_name":"Jean-Pierre A. Kocher","orcid":null},"institutions":[{"id":"https://openalex.org/I1330342723","display_name":"Mayo Clinic","ror":"https://ror.org/02qp3tb03","country_code":"US","type":"funder","lineage":["https://openalex.org/I1330342723"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jean-Pierre A Kocher","raw_affiliation_strings":["Division of Biomedical Statistics & Informatics, Mayo Clinic, Rochester, MN, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Biomedical Statistics & Informatics, Mayo Clinic, Rochester, MN, USA","institution_ids":["https://openalex.org/I1330342723"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027276529","display_name":"David J. Katzmann","orcid":"https://orcid.org/0000-0001-8622-343X"},"institutions":[{"id":"https://openalex.org/I4210125099","display_name":"Mayo Clinic in Arizona","ror":"https://ror.org/03jp40720","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1330342723","https://openalex.org/I4210125099"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"David J Katzmann","raw_affiliation_strings":["Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA","institution_ids":["https://openalex.org/I4210125099"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5109958670","display_name":"Carlos P. Sosa","orcid":null},"institutions":[{"id":"https://openalex.org/I4210120349","display_name":"University of Minnesota Rochester","ror":"https://ror.org/02rh4fw73","country_code":"US","type":"education","lineage":["https://openalex.org/I4210120349"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Carlos P Sosa","raw_affiliation_strings":["Biomedical Informatics and Computational Biology Program, University of Minnesota, Rochester, MN, USA","IBM, Rochester, MN, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biomedical Informatics and Computational Biology Program, University of Minnesota, Rochester, MN, USA","institution_ids":["https://openalex.org/I4210120349"]},{"raw_affiliation_string":"IBM, Rochester, MN, USA","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5109958670"],"corresponding_institution_ids":["https://openalex.org/I4210120349"],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1290,"currency":"GBP","value_usd":1582},"fwci":8.8046,"has_fulltext":true,"cited_by_count":188,"citation_normalized_percentile":{"value":0.98447285,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"3","issue":"1","first_page":"12","last_page":"12"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.8381999731063843,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.8381999731063843,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.03840000182390213,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.020500000566244125,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8984005451202393},{"id":"https://openalex.org/keywords/autodock","display_name":"AutoDock","score":0.8470320105552673},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.7521834373474121},{"id":"https://openalex.org/keywords/multithreading","display_name":"Multithreading","score":0.5905126333236694},{"id":"https://openalex.org/keywords/grid","display_name":"Grid","score":0.4742794930934906},{"id":"https://openalex.org/keywords/supercomputer","display_name":"Supercomputer","score":0.4418202340602875},{"id":"https://openalex.org/keywords/docking","display_name":"Docking (animal)","score":0.4358353912830353},{"id":"https://openalex.org/keywords/multiprocessing","display_name":"Multiprocessing","score":0.4283093214035034},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.31316250562667847},{"id":"https://openalex.org/keywords/thread","display_name":"Thread (computing)","score":0.20325788855552673}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8984005451202393},{"id":"https://openalex.org/C2780152424","wikidata":"https://www.wikidata.org/wiki/Q4826062","display_name":"AutoDock","level":4,"score":0.8470320105552673},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.7521834373474121},{"id":"https://openalex.org/C201410400","wikidata":"https://www.wikidata.org/wiki/Q1064412","display_name":"Multithreading","level":3,"score":0.5905126333236694},{"id":"https://openalex.org/C187691185","wikidata":"https://www.wikidata.org/wiki/Q2020720","display_name":"Grid","level":2,"score":0.4742794930934906},{"id":"https://openalex.org/C83283714","wikidata":"https://www.wikidata.org/wiki/Q121117","display_name":"Supercomputer","level":2,"score":0.4418202340602875},{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.4358353912830353},{"id":"https://openalex.org/C4822641","wikidata":"https://www.wikidata.org/wiki/Q846651","display_name":"Multiprocessing","level":2,"score":0.4283093214035034},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.31316250562667847},{"id":"https://openalex.org/C138101251","wikidata":"https://www.wikidata.org/wiki/Q213092","display_name":"Thread (computing)","level":2,"score":0.20325788855552673},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0},{"id":"https://openalex.org/C159110408","wikidata":"https://www.wikidata.org/wiki/Q121176","display_name":"Nursing","level":1,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.0},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/1758-2946-3-12","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-3-12","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-3-12","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},{"id":"pmid:21527034","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21527034","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of cheminformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:24843e871f614fbb9537242165387009","is_oa":true,"landing_page_url":"https://doaj.org/article/24843e871f614fbb9537242165387009","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Cheminformatics, Vol 3, Iss 1, p 12 (2011)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:3098179","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3098179","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Cheminform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1758-2946-3-12","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-3-12","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-3-12","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Industry, innovation and infrastructure","score":0.4300000071525574,"id":"https://metadata.un.org/sdg/9"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320307762","display_name":"International Business Machines Corporation","ror":"https://ror.org/05hh8d621"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2169244518.pdf","grobid_xml":"https://content.openalex.org/works/W2169244518.grobid-xml"},"referenced_works_count":23,"referenced_works":["https://openalex.org/W121995339","https://openalex.org/W1526205344","https://openalex.org/W1964958542","https://openalex.org/W2003050682","https://openalex.org/W2020084080","https://openalex.org/W2037974485","https://openalex.org/W2039350725","https://openalex.org/W2041046009","https://openalex.org/W2056179306","https://openalex.org/W2058686370","https://openalex.org/W2069944571","https://openalex.org/W2074978477","https://openalex.org/W2089188080","https://openalex.org/W2105668062","https://openalex.org/W2114692946","https://openalex.org/W2135274037","https://openalex.org/W2135904340","https://openalex.org/W2146390839","https://openalex.org/W2152964937","https://openalex.org/W2158534713","https://openalex.org/W2170868211","https://openalex.org/W2176516200","https://openalex.org/W2260133378"],"related_works":["https://openalex.org/W2058674645","https://openalex.org/W1594539819","https://openalex.org/W2766845742","https://openalex.org/W2007257620","https://openalex.org/W4213038553","https://openalex.org/W2130867670","https://openalex.org/W1984029386","https://openalex.org/W4312202637","https://openalex.org/W2374902472","https://openalex.org/W2136513242"],"abstract_inverted_index":{"BACKGROUND:":[0],"Virtual":[1],"(computational)":[2],"screening":[3,141],"is":[4,13,28,129,177],"an":[5],"increasingly":[6],"important":[7],"tool":[8],"for":[9,18,65],"drug":[10],"discovery.":[11],"AutoDock":[12,27,53,61],"a":[14,29,49],"popular":[15],"open-source":[16],"application":[17],"performing":[19],"molecular":[20,187],"docking,":[21],"the":[22,41,73,121,152,169,183,192,196],"prediction":[23],"of":[24,40,52,75,101,132,144,154,156,172,185,198],"ligand-receptor":[25],"interactions.":[26],"serial":[30],"application,":[31],"though":[32],"several":[33],"previous":[34],"efforts":[35],"have":[36],"parallelized":[37,64],"various":[38],"aspects":[39],"program.":[42],"In":[43,79,125],"this":[44],"paper,":[45],"we":[46],"report":[47],"on":[48,67,105,120],"multi-level":[50],"parallelization":[51,165,204],"4.2":[54,62],"(mpAD4).":[55],"RESULTS:":[56],"Using":[57,110],"MPI":[58,111,164],"and":[59,70,139,160,190,201,210],"OpenMP,":[60],"was":[63,82,103],"use":[66],"MPI-enabled":[68],"systems":[69,123],"to":[71,84,98,194,205],"multithread":[72],"execution":[74,155,170,184],"individual":[76,157],"docking":[77,97,158,188],"jobs.":[78],"addition,":[80],"code":[81],"implemented":[83],"reduce":[85,168],"input/output":[86],"(I/O)":[87],"traffic":[88],"by":[89],"reusing":[90],"grid":[91,133],"maps":[92,134],"at":[93],"each":[94],"node":[95],"from":[96],"docking.":[99],"Performance":[100],"mpAD4":[102,115,181],"examined":[104],"two":[106],"multiprocessor":[107,122],"computers.":[108],"CONCLUSIONS:":[109],"with":[112,117,149,163],"OpenMP":[113,150],"multithreading,":[114],"scales":[116],"near":[118],"linearity":[119],"tested.":[124],"situations":[126],"where":[127],"I/O":[128,138],"limiting,":[130],"reuse":[131],"reduces":[135],"both":[136,208],"system":[137],"overall":[140],"time.":[142],"Multithreading":[143],"AutoDock's":[145],"Lamarkian":[146],"Genetic":[147],"Algorithm":[148],"increases":[151],"speed":[153],"jobs,":[159],"when":[161],"combined":[162],"can":[166],"significantly":[167],"time":[171],"virtual":[173],"screens.":[174],"This":[175],"work":[176],"significant":[178],"in":[179],"that":[180],"speeds":[182],"certain":[186],"workloads":[189,209],"allows":[191],"user":[193],"optimize":[195],"degree":[197],"system-level":[199],"(MPI)":[200],"node-level":[202],"(OpenMP)":[203],"best":[206],"fit":[207],"computational":[211],"resources.":[212]},"counts_by_year":[{"year":2026,"cited_by_count":8},{"year":2025,"cited_by_count":11},{"year":2024,"cited_by_count":22},{"year":2023,"cited_by_count":24},{"year":2022,"cited_by_count":16},{"year":2021,"cited_by_count":14},{"year":2020,"cited_by_count":18},{"year":2019,"cited_by_count":7},{"year":2018,"cited_by_count":12},{"year":2017,"cited_by_count":11},{"year":2016,"cited_by_count":11},{"year":2015,"cited_by_count":7},{"year":2014,"cited_by_count":12},{"year":2013,"cited_by_count":8},{"year":2012,"cited_by_count":7}],"updated_date":"2026-05-29T09:21:14.243279","created_date":"2025-10-10T00:00:00"}