{"id":"https://openalex.org/W2108389384","doi":"https://doi.org/10.1093/bioinformatics/btv082","title":"Fast, accurate, and reliable molecular docking with QuickVina 2","display_name":"Fast, accurate, and reliable molecular docking with QuickVina 2","publication_year":2015,"publication_date":"2015-02-24","ids":{"openalex":"https://openalex.org/W2108389384","doi":"https://doi.org/10.1093/bioinformatics/btv082","mag":"2108389384","pmid":"https://pubmed.ncbi.nlm.nih.gov/25717194"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btv082","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv082","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/13/2214/49034896/bioinformatics_31_13_2214.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/31/13/2214/49034896/bioinformatics_31_13_2214.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5089380873","display_name":"Amr Alhossary","orcid":"https://orcid.org/0000-0002-4470-5817"},"institutions":[{"id":"https://openalex.org/I172675005","display_name":"Nanyang Technological University","ror":"https://ror.org/02e7b5302","country_code":"SG","type":"education","lineage":["https://openalex.org/I172675005"]},{"id":"https://openalex.org/I79891267","display_name":"Singapore Management University","ror":"https://ror.org/050qmg959","country_code":"SG","type":"education","lineage":["https://openalex.org/I79891267"]}],"countries":["SG"],"is_corresponding":true,"raw_author_name":"Amr Alhossary","raw_affiliation_strings":["1 School of Computer Engineering, Nanyang Technological University, Singapore 639798, 2School of Information Systems, Singapore Management University, Singapore 188065, and 3School of Biological Sciences, Nanyang Technological University, Singapore 637551"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 School of Computer Engineering, Nanyang Technological University, Singapore 639798, 2School of Information Systems, Singapore Management University, Singapore 188065, and 3School of Biological Sciences, Nanyang Technological University, Singapore 637551","institution_ids":["https://openalex.org/I172675005","https://openalex.org/I79891267"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083689711","display_name":"Stephanus Daniel Handoko","orcid":null},"institutions":[{"id":"https://openalex.org/I172675005","display_name":"Nanyang Technological University","ror":"https://ror.org/02e7b5302","country_code":"SG","type":"education","lineage":["https://openalex.org/I172675005"]},{"id":"https://openalex.org/I79891267","display_name":"Singapore Management University","ror":"https://ror.org/050qmg959","country_code":"SG","type":"education","lineage":["https://openalex.org/I79891267"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Stephanus Daniel Handoko","raw_affiliation_strings":["1 School of Computer Engineering, Nanyang Technological University, Singapore 639798, 2School of Information Systems, Singapore Management University, Singapore 188065, and 3School of Biological Sciences, Nanyang Technological University, Singapore 637551"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 School of Computer Engineering, Nanyang Technological University, Singapore 639798, 2School of Information Systems, Singapore Management University, Singapore 188065, and 3School of Biological Sciences, Nanyang Technological University, Singapore 637551","institution_ids":["https://openalex.org/I172675005","https://openalex.org/I79891267"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071286986","display_name":"Yuguang Mu","orcid":"https://orcid.org/0000-0002-2499-026X"},"institutions":[{"id":"https://openalex.org/I79891267","display_name":"Singapore Management University","ror":"https://ror.org/050qmg959","country_code":"SG","type":"education","lineage":["https://openalex.org/I79891267"]},{"id":"https://openalex.org/I172675005","display_name":"Nanyang Technological University","ror":"https://ror.org/02e7b5302","country_code":"SG","type":"education","lineage":["https://openalex.org/I172675005"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Yuguang Mu","raw_affiliation_strings":["1 School of Computer Engineering, Nanyang Technological University, Singapore 639798, 2School of Information Systems, Singapore Management University, Singapore 188065, and 3School of Biological Sciences, Nanyang Technological University, Singapore 637551"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 School of Computer Engineering, Nanyang Technological University, Singapore 639798, 2School of Information Systems, Singapore Management University, Singapore 188065, and 3School of Biological Sciences, Nanyang Technological University, Singapore 637551","institution_ids":["https://openalex.org/I172675005","https://openalex.org/I79891267"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5027208445","display_name":"Chee Keong Kwoh","orcid":"https://orcid.org/0000-0002-8547-6387"},"institutions":[{"id":"https://openalex.org/I79891267","display_name":"Singapore Management University","ror":"https://ror.org/050qmg959","country_code":"SG","type":"education","lineage":["https://openalex.org/I79891267"]},{"id":"https://openalex.org/I172675005","display_name":"Nanyang Technological University","ror":"https://ror.org/02e7b5302","country_code":"SG","type":"education","lineage":["https://openalex.org/I172675005"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Chee-Keong Kwoh","raw_affiliation_strings":["1 School of Computer Engineering, Nanyang Technological University, Singapore 639798, 2School of Information Systems, Singapore Management University, Singapore 188065, and 3School of Biological Sciences, Nanyang Technological University, Singapore 637551"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 School of Computer Engineering, Nanyang Technological University, Singapore 639798, 2School of Information Systems, Singapore Management University, Singapore 188065, and 3School of Biological Sciences, Nanyang Technological University, Singapore 637551","institution_ids":["https://openalex.org/I172675005","https://openalex.org/I79891267"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5089380873"],"corresponding_institution_ids":["https://openalex.org/I172675005","https://openalex.org/I79891267"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":3.9976,"has_fulltext":true,"cited_by_count":365,"citation_normalized_percentile":{"value":0.94067211,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"31","issue":"13","first_page":"2214","last_page":"2216"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9627000093460083,"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":0.9627000093460083,"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":0.01940000057220459,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.0017000000225380063,"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/docking","display_name":"Docking (animal)","score":0.6402201056480408},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6091077923774719},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3580257296562195},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3228747248649597},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.13609349727630615},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.10304006934165955}],"concepts":[{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.6402201056480408},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6091077923774719},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3580257296562195},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3228747248649597},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.13609349727630615},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.10304006934165955},{"id":"https://openalex.org/C159110408","wikidata":"https://www.wikidata.org/wiki/Q121176","display_name":"Nursing","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","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":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D062313","descriptor_name":"Databases, Pharmaceutical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062313","descriptor_name":"Databases, Pharmaceutical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062313","descriptor_name":"Databases, Pharmaceutical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btv082","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv082","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/13/2214/49034896/bioinformatics_31_13_2214.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:25717194","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25717194","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:ink.library.smu.edu.sg:sis_research-4257","is_oa":false,"landing_page_url":"https://ink.library.smu.edu.sg/sis_research/3255","pdf_url":null,"source":{"id":"https://openalex.org/S4377196871","display_name":"Institutional Knowledge (InK) - Institutional Knowledge at Singapore Management University (Singapore Management University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I79891267","host_organization_name":"Singapore Management University","host_organization_lineage":["https://openalex.org/I79891267"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"https://doi.org/10.1093/bioinformatics/btv082","raw_type":"Journal Article"},{"id":"pmh:oai:open-archive.highwire.org:bioinfo:31/13/2214","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/31/13/2214","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btv082","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv082","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/13/2214/49034896/bioinformatics_31_13_2214.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/7","score":0.6200000047683716,"display_name":"Affordable and clean energy"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320320766","display_name":"Nanyang Technological University","ror":"https://ror.org/02e7b5302"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2108389384.pdf","grobid_xml":"https://content.openalex.org/works/W2108389384.grobid-xml"},"referenced_works_count":3,"referenced_works":["https://openalex.org/W1993046136","https://openalex.org/W1993403967","https://openalex.org/W2134967712"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052"],"abstract_inverted_index":{"MOTIVATION:":[0],"The":[1,201],"need":[2],"for":[3,8,31,121,127,141],"efficient":[4],"molecular":[5],"docking":[6,27],"tools":[7],"high-throughput":[9],"screening":[10],"is":[11,23,208],"growing":[12],"alongside":[13],"the":[14,39,59,69,75,78,84,90,97,122,128,136,151,157,167,178,191],"rapid":[15],"growth":[16],"of":[17,62,71,77,86,93,101,107,112,119,130,147,166,173,190,205],"drug-fragment":[18],"databases.":[19],"AutoDock":[20],"Vina":[21,102,159],"('Vina')":[22],"a":[24,42,105,116],"widely":[25],"used":[26],"tool":[28],"with":[29,115,144,169],"parallelization":[30],"speed.":[32],"QuickVina":[33,63],"('QVina":[34,64],"1')":[35],"then":[36],"further":[37],"enhanced":[38],"speed":[40,70],"via":[41],"heuristics,":[43],"requiring":[44],"high":[45],"exhaustiveness.":[46],"With":[47,96],"low":[48],"exhaustiveness,":[49],"its":[50],"accuracy":[51],"was":[52,154],"compromised.":[53],"We":[54,82],"present":[55],"in":[56],"this":[57],"article":[58],"latest":[60],"version":[61],"2')":[65],"that":[66],"inherits":[67],"both":[68],"QVina":[72,87,162,194,206],"1":[73],"and":[74,109,125],"reliability":[76],"original":[79,137],"Vina.":[80,138],"RESULTS:":[81],"tested":[83],"efficacy":[85],"2":[88,163,186,195,207],"on":[89,164,188],"core":[91],"set":[92],"PDBbind":[94],"2014.":[95],"default":[98],"exhaustiveness":[99],"level":[100],"(i.e.":[103],"8),":[104],"maximum":[106],"20.49-fold":[108],"an":[110],"average":[111,170],"2.30-fold":[113],"acceleration":[114,143],"correlation":[117],"coefficient":[118],"0.967":[120],"first":[123],"mode":[124],"0.911":[126],"sum":[129],"all":[131],"modes":[132],"were":[133],"attained":[134,196],"over":[135,161],"A":[139],"tendency":[140],"higher":[142],"increased":[145],"number":[146],"rotatable":[148],"bonds":[149],"as":[150],"design":[152],"variables":[153],"observed.":[155],"On":[156,177],"accuracy,":[158],"wins":[160],"30%":[165],"data":[168,192,217],"energy":[171],"difference":[172],"only":[174],"0.58":[175],"kcal/mol.":[176],"same":[179],"dataset,":[180],"GOLD":[181],"produced":[182],"RMSD":[183],"smaller":[184],"than":[185],"\u00c5":[187],"56.9%":[189],"while":[193],"63.1%.":[197],"AVAILABILITY":[198],"AND":[199],"IMPLEMENTATION:":[200],"C++":[202],"source":[203],"code":[204],"available":[209,219],"at":[210,220],"(www.qvina.org).":[211],"CONTACT:":[212],"aalhossary@pmail.ntu.edu.sg":[213],"SUPPLEMENTARY":[214],"INFORMATION:":[215],"Supplementary":[216],"are":[218],"Bioinformatics":[221],"online.":[222]},"counts_by_year":[{"year":2026,"cited_by_count":34},{"year":2025,"cited_by_count":62},{"year":2024,"cited_by_count":62},{"year":2023,"cited_by_count":68},{"year":2022,"cited_by_count":57},{"year":2021,"cited_by_count":37},{"year":2020,"cited_by_count":26},{"year":2019,"cited_by_count":7},{"year":2018,"cited_by_count":6},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":3}],"updated_date":"2026-05-09T13:55:54.758798","created_date":"2025-10-10T00:00:00"}
