{"id":"https://openalex.org/W4366241519","doi":"https://doi.org/10.1021/acs.jcim.3c00031","title":"Large-Scale Docking in the Cloud","display_name":"Large-Scale Docking in the Cloud","publication_year":2023,"publication_date":"2023-04-18","ids":{"openalex":"https://openalex.org/W4366241519","doi":"https://doi.org/10.1021/acs.jcim.3c00031","pmid":"https://pubmed.ncbi.nlm.nih.gov/37071086"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.3c00031","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.3c00031","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"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 Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://doi.org/10.1021/acs.jcim.3c00031","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5048727010","display_name":"Benjamin I. Tingle","orcid":null},"institutions":[{"id":"https://openalex.org/I180670191","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Benjamin I. Tingle","raw_affiliation_strings":["Department of Pharmaceutical Chemistry, University of California San Francisco, 1700 4th Street, MC 2550, San Francisco, California 94158-2330, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pharmaceutical Chemistry, University of California San Francisco, 1700 4th Street, MC 2550, San Francisco, California 94158-2330, United States","institution_ids":["https://openalex.org/I180670191"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5054045417","display_name":"John J. Irwin","orcid":"https://orcid.org/0000-0002-1195-6417"},"institutions":[{"id":"https://openalex.org/I180670191","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"John J. Irwin","raw_affiliation_strings":["Department of Pharmaceutical Chemistry, University of California San Francisco, 1700 4th Street, MC 2550, San Francisco, California 94158-2330, United States"],"raw_orcid":"https://orcid.org/0000-0002-1195-6417","affiliations":[{"raw_affiliation_string":"Department of Pharmaceutical Chemistry, University of California San Francisco, 1700 4th Street, MC 2550, San Francisco, California 94158-2330, United States","institution_ids":["https://openalex.org/I180670191"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5054045417"],"corresponding_institution_ids":["https://openalex.org/I180670191"],"apc_list":null,"apc_paid":null,"fwci":5.1709,"has_fulltext":true,"cited_by_count":27,"citation_normalized_percentile":{"value":0.96296914,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"63","issue":"9","first_page":"2735","last_page":"2741"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9986000061035156,"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":0.9986000061035156,"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/T11407","display_name":"Innovative Microfluidic and Catalytic Techniques Innovation","score":0.9829000234603882,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12867","display_name":"Advanced Biosensing Techniques and Applications","score":0.9632999897003174,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/dock","display_name":"DOCK","score":0.9786157608032227},{"id":"https://openalex.org/keywords/docking","display_name":"Docking (animal)","score":0.7815461158752441},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.7665022611618042},{"id":"https://openalex.org/keywords/cloud-computing","display_name":"Cloud computing","score":0.7016076445579529},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6594516038894653},{"id":"https://openalex.org/keywords/exploit","display_name":"Exploit","score":0.5432780981063843},{"id":"https://openalex.org/keywords/autodock","display_name":"AutoDock","score":0.42902588844299316},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.3108396530151367},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.2911650538444519},{"id":"https://openalex.org/keywords/computer-security","display_name":"Computer security","score":0.08585295081138611}],"concepts":[{"id":"https://openalex.org/C93073132","wikidata":"https://www.wikidata.org/wiki/Q24726581","display_name":"DOCK","level":2,"score":0.9786157608032227},{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.7815461158752441},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.7665022611618042},{"id":"https://openalex.org/C79974875","wikidata":"https://www.wikidata.org/wiki/Q483639","display_name":"Cloud computing","level":2,"score":0.7016076445579529},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6594516038894653},{"id":"https://openalex.org/C165696696","wikidata":"https://www.wikidata.org/wiki/Q11287","display_name":"Exploit","level":2,"score":0.5432780981063843},{"id":"https://openalex.org/C2780152424","wikidata":"https://www.wikidata.org/wiki/Q4826062","display_name":"AutoDock","level":4,"score":0.42902588844299316},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.3108396530151367},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.2911650538444519},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"score":0.08585295081138611},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","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/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"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/C159110408","wikidata":"https://www.wikidata.org/wiki/Q121176","display_name":"Nursing","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1021/acs.jcim.3c00031","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.3c00031","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"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 Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:37071086","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37071086","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 chemical information and modeling","raw_type":null},{"id":"pmh:oai:escholarship.org:ark:/13030/qt2223q35s","is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/2223q35s","pdf_url":"https://escholarship.org/content/qt2223q35s/qt2223q35s.pdf?t=rxtwqm","source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"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":"Journal of Chemical Information and Modeling, vol 63, iss 9","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:10170500","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10170500","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10170500/pdf/ci3c00031.pdf","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 Chem Inf Model","raw_type":"Text"},{"id":"pmh:ark:/13030/qt2223q35s","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null}],"best_oa_location":{"id":"doi:10.1021/acs.jcim.3c00031","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.3c00031","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"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 Chemical Information and Modeling","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9","score":0.5299999713897705}],"awards":[{"id":"https://openalex.org/G1890007942","display_name":null,"funder_award_id":"GM133836","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G653760849","display_name":null,"funder_award_id":"GM133836","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":20,"referenced_works":["https://openalex.org/W1983376893","https://openalex.org/W2912171584","https://openalex.org/W3004731690","https://openalex.org/W3010016408","https://openalex.org/W3035777330","https://openalex.org/W3108778136","https://openalex.org/W3120407713","https://openalex.org/W3126031592","https://openalex.org/W3165388098","https://openalex.org/W3200170115","https://openalex.org/W3201539868","https://openalex.org/W3209170263","https://openalex.org/W4200233821","https://openalex.org/W4200289210","https://openalex.org/W4210617107","https://openalex.org/W4229365929","https://openalex.org/W4297497355","https://openalex.org/W4297995910","https://openalex.org/W4306948725","https://openalex.org/W4320857994"],"related_works":["https://openalex.org/W2167041509","https://openalex.org/W4393450381","https://openalex.org/W4282913408","https://openalex.org/W2100436540","https://openalex.org/W2058674645","https://openalex.org/W2300502530","https://openalex.org/W3201417569","https://openalex.org/W1594539819","https://openalex.org/W2766845742","https://openalex.org/W2149658535"],"abstract_inverted_index":{"Molecular":[0],"docking":[1,61,145,162],"is":[2,22,147,178],"a":[3,36,59,112,124],"pragmatic":[4],"approach":[5,47],"to":[6,25,63,98,157,167,173],"exploit":[7],"protein":[8],"structures":[9],"for":[10,38,132,160,180],"new":[11,141],"ligand":[12],"discovery,":[13],"but":[14],"the":[15,43,49,81,137,165],"growing":[16],"size":[17],"of":[18,54,66,89,139],"available":[19,171],"chemical":[20],"space":[21],"increasingly":[23],"challenging":[24],"screen":[26,64],"on":[27,116,127],"in-house":[28],"computer":[29],"clusters.":[30],"We":[31,69,95],"have":[32],"therefore":[33],"developed":[34],"AWS-DOCK,":[35],"protocol":[37,146],"running":[39],"UCSF":[40],"DOCK":[41,176],"in":[42,101,122,130,149],"AWS":[44,104,131],"cloud.":[45],"Our":[46],"leverages":[48],"low":[50],"cost":[51,102,138],"and":[52,152],"scalability":[53],"cloud":[55,144],"resources":[56],"combined":[57],"with":[58,84],"low-molecule-cost":[60],"engine":[62],"billions":[65],"molecules":[67,79],"efficiently.":[68],"benchmarked":[70],"our":[71,117],"system":[72],"by":[73],"screening":[74],"50":[75],"million":[76],"HAC":[77],"22":[78],"against":[80],"DRD4":[82],"receptor":[83],"an":[85],"average":[86],"CPU":[87],"time":[88],"around":[90,133],"1":[91],"s":[92],"per":[93],"molecule.":[94],"saw":[96],"up":[97],"3-fold":[99],"variations":[100],"between":[103],"availability":[105],"zones.":[106],"Docking":[107],"4.5":[108],"billion":[109],"lead-like":[110],"molecules,":[111],"7":[113],"week":[114,125],"calculation":[115],"1000-core":[118],"lab":[119],"cluster,":[120],"runs":[121],"about":[123],"depending":[126],"accessible":[128],"CPUs,":[129],"$25,000,":[134],"less":[135],"than":[136],"two":[140],"nodes.":[142],"The":[143],"described":[148],"easy-to-follow":[150],"steps":[151],"may":[153],"be":[154,158],"sufficiently":[155],"general":[156],"used":[159],"other":[161],"programs.":[163],"All":[164],"tools":[166],"enable":[168],"AWS-DOCK":[169],"are":[170],"free":[172,179],"everyone,":[174],"while":[175],"3.8":[177],"academic":[181],"research.":[182]},"counts_by_year":[{"year":2026,"cited_by_count":6},{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":12},{"year":2023,"cited_by_count":2}],"updated_date":"2026-05-14T08:36:36.166977","created_date":"2025-10-10T00:00:00"}