{"id":"https://openalex.org/W4386585097","doi":"https://doi.org/10.1145/3569951.3597599","title":"Scalable and Reproducible Virtual Screening through an API-Integrated Workflow","display_name":"Scalable and Reproducible Virtual Screening through an API-Integrated Workflow","publication_year":2023,"publication_date":"2023-07-23","ids":{"openalex":"https://openalex.org/W4386585097","doi":"https://doi.org/10.1145/3569951.3597599"},"language":"en","primary_location":{"id":"doi:10.1145/3569951.3597599","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3569951.3597599","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3569951.3597599","source":{"id":"https://openalex.org/S4306523034","display_name":"Practice and Experience in Advanced Research Computing","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Practice and Experience in Advanced Research Computing","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://dl.acm.org/doi/pdf/10.1145/3569951.3597599","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5064844764","display_name":"T.R. Huff","orcid":"https://orcid.org/0000-0003-2849-8093"},"institutions":[{"id":"https://openalex.org/I4388891828","display_name":"Texas Advanced Computing Center","ror":"https://ror.org/00xg4bh43","country_code":null,"type":"facility","lineage":["https://openalex.org/I4388891828","https://openalex.org/I86519309"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Tiffany Huff","raw_affiliation_strings":["Texas Advanced Computing Center, USA"],"raw_orcid":"https://orcid.org/0000-0003-2849-8093","affiliations":[{"raw_affiliation_string":"Texas Advanced Computing Center, USA","institution_ids":["https://openalex.org/I4388891828"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5092841059","display_name":"Austin Darrow","orcid":"https://orcid.org/0009-0008-5560-0472"},"institutions":[{"id":"https://openalex.org/I4388891828","display_name":"Texas Advanced Computing Center","ror":"https://ror.org/00xg4bh43","country_code":null,"type":"facility","lineage":["https://openalex.org/I4388891828","https://openalex.org/I86519309"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Austin Darrow","raw_affiliation_strings":["Texas Advanced Computing Center, USA"],"raw_orcid":"https://orcid.org/0009-0008-5560-0472","affiliations":[{"raw_affiliation_string":"Texas Advanced Computing Center, USA","institution_ids":["https://openalex.org/I4388891828"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Joshua Medina","orcid":"https://orcid.org/0009-0002-4049-5039"},"institutions":[{"id":"https://openalex.org/I4388891828","display_name":"Texas Advanced Computing Center","ror":"https://ror.org/00xg4bh43","country_code":null,"type":"facility","lineage":["https://openalex.org/I4388891828","https://openalex.org/I86519309"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Joshua Medina","raw_affiliation_strings":["Texas Advanced Computing Center, USA"],"raw_orcid":"https://orcid.org/0009-0002-4049-5039","affiliations":[{"raw_affiliation_string":"Texas Advanced Computing Center, USA","institution_ids":["https://openalex.org/I4388891828"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090195616","display_name":"Erik Ferlanti","orcid":"https://orcid.org/0000-0001-5128-1584"},"institutions":[{"id":"https://openalex.org/I4388891828","display_name":"Texas Advanced Computing Center","ror":"https://ror.org/00xg4bh43","country_code":null,"type":"facility","lineage":["https://openalex.org/I4388891828","https://openalex.org/I86519309"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Erik Ferlanti","raw_affiliation_strings":["Texas Advanced Computing Center, USA"],"raw_orcid":"https://orcid.org/0000-0001-5128-1584","affiliations":[{"raw_affiliation_string":"Texas Advanced Computing Center, USA","institution_ids":["https://openalex.org/I4388891828"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078550956","display_name":"James P. Carson","orcid":"https://orcid.org/0000-0001-9009-5645"},"institutions":[{"id":"https://openalex.org/I4388891828","display_name":"Texas Advanced Computing Center","ror":"https://ror.org/00xg4bh43","country_code":null,"type":"facility","lineage":["https://openalex.org/I4388891828","https://openalex.org/I86519309"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"James Carson","raw_affiliation_strings":["Texas Advanced Computing Center, USA"],"raw_orcid":"https://orcid.org/0000-0001-9009-5645","affiliations":[{"raw_affiliation_string":"Texas Advanced Computing Center, USA","institution_ids":["https://openalex.org/I4388891828"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051814524","display_name":"John Fonner","orcid":"https://orcid.org/0000-0003-4398-2916"},"institutions":[{"id":"https://openalex.org/I4388891828","display_name":"Texas Advanced Computing Center","ror":"https://ror.org/00xg4bh43","country_code":null,"type":"facility","lineage":["https://openalex.org/I4388891828","https://openalex.org/I86519309"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"John Fonner","raw_affiliation_strings":["Texas Advanced Computing Center, USA"],"raw_orcid":"https://orcid.org/0000-0003-4398-2916","affiliations":[{"raw_affiliation_string":"Texas Advanced Computing Center, USA","institution_ids":["https://openalex.org/I4388891828"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5092841060","display_name":"Sal Tijerina","orcid":"https://orcid.org/0009-0001-9283-965X"},"institutions":[{"id":"https://openalex.org/I4388891828","display_name":"Texas Advanced Computing Center","ror":"https://ror.org/00xg4bh43","country_code":null,"type":"facility","lineage":["https://openalex.org/I4388891828","https://openalex.org/I86519309"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sal Tijerina","raw_affiliation_strings":["Texas Advanced Computing Center, USA"],"raw_orcid":"https://orcid.org/0009-0001-9283-965X","affiliations":[{"raw_affiliation_string":"Texas Advanced Computing Center, USA","institution_ids":["https://openalex.org/I4388891828"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017815970","display_name":"Stanley J. Watowich","orcid":"https://orcid.org/0000-0002-1660-1818"},"institutions":[{"id":"https://openalex.org/I55302922","display_name":"The University of Texas Medical Branch at Galveston","ror":"https://ror.org/016tfm930","country_code":"US","type":"education","lineage":["https://openalex.org/I55302922"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Stanley J. Watowich","raw_affiliation_strings":["University of Texas Medical Branch, USA"],"raw_orcid":"https://orcid.org/0000-0002-1660-1818","affiliations":[{"raw_affiliation_string":"University of Texas Medical Branch, USA","institution_ids":["https://openalex.org/I55302922"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5002844924","display_name":"William J. Allen","orcid":"https://orcid.org/0000-0003-1322-2764"},"institutions":[{"id":"https://openalex.org/I4388891828","display_name":"Texas Advanced Computing Center","ror":"https://ror.org/00xg4bh43","country_code":null,"type":"facility","lineage":["https://openalex.org/I4388891828","https://openalex.org/I86519309"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"William J. Allen","raw_affiliation_strings":["Texas Advanced Computing Center, USA"],"raw_orcid":"https://orcid.org/0000-0003-1322-2764","affiliations":[{"raw_affiliation_string":"Texas Advanced Computing Center, USA","institution_ids":["https://openalex.org/I4388891828"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5064844764"],"corresponding_institution_ids":["https://openalex.org/I4388891828"],"apc_list":null,"apc_paid":null,"fwci":1.6178,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.89970384,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":null,"issue":null,"first_page":"196","last_page":"199"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.9972000122070312,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},"topics":[{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.9972000122070312,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9819999933242798,"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":0.9433000087738037,"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/computer-science","display_name":"Computer science","score":0.8298483490943909},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.7648043036460876},{"id":"https://openalex.org/keywords/virtual-screening","display_name":"Virtual screening","score":0.6404876112937927},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.6308934688568115},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.6171544194221497},{"id":"https://openalex.org/keywords/supercomputer","display_name":"Supercomputer","score":0.5622009038925171},{"id":"https://openalex.org/keywords/cyberinfrastructure","display_name":"Cyberinfrastructure","score":0.558854877948761},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.47763100266456604},{"id":"https://openalex.org/keywords/application-programming-interface","display_name":"Application programming interface","score":0.4373655915260315},{"id":"https://openalex.org/keywords/distributed-computing","display_name":"Distributed computing","score":0.3602641820907593},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.3514336347579956},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.3248366713523865},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.27732715010643005},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.2636694014072418},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.1470799446105957}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8298483490943909},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.7648043036460876},{"id":"https://openalex.org/C103697762","wikidata":"https://www.wikidata.org/wiki/Q4112105","display_name":"Virtual screening","level":3,"score":0.6404876112937927},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.6308934688568115},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.6171544194221497},{"id":"https://openalex.org/C83283714","wikidata":"https://www.wikidata.org/wiki/Q121117","display_name":"Supercomputer","level":2,"score":0.5622009038925171},{"id":"https://openalex.org/C2776397876","wikidata":"https://www.wikidata.org/wiki/Q1450531","display_name":"Cyberinfrastructure","level":2,"score":0.558854877948761},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.47763100266456604},{"id":"https://openalex.org/C99613125","wikidata":"https://www.wikidata.org/wiki/Q165194","display_name":"Application programming interface","level":2,"score":0.4373655915260315},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.3602641820907593},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.3514336347579956},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.3248366713523865},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.27732715010643005},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.2636694014072418},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.1470799446105957},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3569951.3597599","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3569951.3597599","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3569951.3597599","source":{"id":"https://openalex.org/S4306523034","display_name":"Practice and Experience in Advanced Research Computing","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Practice and Experience in Advanced Research Computing","raw_type":"proceedings-article"}],"best_oa_location":{"id":"doi:10.1145/3569951.3597599","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3569951.3597599","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3569951.3597599","source":{"id":"https://openalex.org/S4306523034","display_name":"Practice and Experience in Advanced Research Computing","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Practice and Experience in Advanced Research Computing","raw_type":"proceedings-article"},"sustainable_development_goals":[{"score":0.41999998688697815,"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure"}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4386585097.pdf","grobid_xml":"https://content.openalex.org/works/W4386585097.grobid-xml"},"referenced_works_count":15,"referenced_works":["https://openalex.org/W1899011294","https://openalex.org/W2037127688","https://openalex.org/W2093426296","https://openalex.org/W2105668062","https://openalex.org/W2127760066","https://openalex.org/W2131174104","https://openalex.org/W2134967712","https://openalex.org/W2296575546","https://openalex.org/W2578119541","https://openalex.org/W3083406432","https://openalex.org/W3094640617","https://openalex.org/W3156001951","https://openalex.org/W3164436820","https://openalex.org/W3168436232","https://openalex.org/W3209471044"],"related_works":["https://openalex.org/W273500195","https://openalex.org/W2043019925","https://openalex.org/W4236056781","https://openalex.org/W4399254454","https://openalex.org/W4293768956","https://openalex.org/W2773781927","https://openalex.org/W2184477657","https://openalex.org/W90628286","https://openalex.org/W1696735061","https://openalex.org/W2152811545"],"abstract_inverted_index":{"Virtual":[0],"screening":[1,58,90,229],"is":[2,59,242],"a":[3,27,98,133,226],"key":[4],"step":[5],"of":[6,19,26,35,72,149,187,209],"the":[7,17,23,69,94,144,147,185,193,210,214,222,255],"drug":[8,73,228],"discovery":[9],"process":[10],"which":[11],"utilizes":[12],"computational":[13],"resources":[14,67],"to":[15,65,87,93,112,142,191,198,224,244],"simulate":[16],"behavior":[18],"small":[20,163],"molecules":[21,36,164],"in":[22,61,68,237],"binding":[24],"site":[25],"target":[28],"protein.":[29],"[13]":[30],"Researchers":[31],"often":[32],"test":[33],"millions":[34],"when":[37,204],"searching":[38],"for":[39,56,63,137,172,200],"an":[40,77],"early":[41,70],"hit":[42],"compound,":[43],"requiring":[44],"significant":[45],"CPU":[46],"hours.":[47,239],"An":[48],"accessible,":[49],"convenient,":[50],"fast,":[51],"and":[52,169,217,230,248],"computationally":[53],"efficient":[54,195],"means":[55],"virtual":[57,89,227],"desirable":[60],"order":[62],"researchers":[64,86],"conserve":[66],"phase":[71],"discovery.":[74],"We":[75],"developed":[76],"application":[78],"programming":[79],"interface":[80],"(API)":[81],"integrated":[82],"workflow":[83,104,145],"that":[84],"allows":[85],"submit":[88],"batch":[91,206],"jobs":[92],"Lonestar6":[95],"supercomputer":[96],"through":[97],"web":[99,155],"portal.":[100,156],"The":[101,123,240],"containerized":[102],"[7]":[103],"employs":[105],"parallelized":[106],"Python":[107],"scripting":[108],"using":[109],"mpi4py":[110],"[2]":[111],"efficiently":[113],"distribute":[114],"molecular":[115],"docking":[116,235],"tasks":[117],"performed":[118],"by":[119],"AutoDock":[120],"Vina.":[121],"[3]":[122],"Texas":[124,150],"Advanced":[125],"Computing":[126],"Center":[127],"(TACC)":[128],"API":[129,135],"(TAPIS)":[130],"framework":[131,136],"[16],":[132],"REST":[134],"research":[138],"computing,":[139],"was":[140],"used":[141],"integrate":[143],"into":[146],"University":[148],"System":[151],"Research":[152],"Cyberinfrastructure":[153],"(UTRC)":[154],"[12]":[157],"Five":[158],"large":[159],"libraries":[160],"representing":[161],"commercially-available":[162],"or":[165],"fragments":[166],"were":[167],"prepared":[168],"are":[170],"available":[171,243],"screening.":[173],"Here,":[174],"we":[175],"discuss":[176],"our":[177],"experience":[178],"developing":[179],"this":[180],"service,":[181],"as":[182,184],"well":[183],"results":[186],"extensive":[188],"internal":[189],"benchmarks":[190],"determine":[192],"most":[194],"parallelization":[196],"scheme":[197],"employ":[199],"each":[201],"molecule":[202],"library":[203],"submitting":[205],"jobs.":[207],"Regardless":[208],"chosen":[211],"ligand":[212],"library,":[213],"core,":[215],"node,":[216],"parallel":[218],"task":[219],"specifications":[220],"allow":[221],"user":[223],"run":[225],"receive":[231],"their":[232],"resulting":[233],"top":[234],"scores":[236],"24":[238],"service":[241],"registered":[245],"academic":[246],"users,":[247],"more":[249],"information":[250],"can":[251],"be":[252],"found":[253],"at":[254,258],"Drug":[256],"Discovery":[257],"TACC":[259],"website.":[260],"[18]":[261]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2023,"cited_by_count":1}],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}
