{"id":"https://openalex.org/W4402829784","doi":"https://doi.org/10.1109/tcbb.2024.3467127","title":"Vina-GPU 2.1: Towards Further Optimizing Docking Speed and Precision of AutoDock Vina and Its Derivatives","display_name":"Vina-GPU 2.1: Towards Further Optimizing Docking Speed and Precision of AutoDock Vina and Its Derivatives","publication_year":2024,"publication_date":"2024-09-25","ids":{"openalex":"https://openalex.org/W4402829784","doi":"https://doi.org/10.1109/tcbb.2024.3467127","pmid":"https://pubmed.ncbi.nlm.nih.gov/39320991"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2024.3467127","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2024.3467127","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5087976552","display_name":"Shidi Tang","orcid":"https://orcid.org/0000-0001-5493-7411"},"institutions":[{"id":"https://openalex.org/I41198531","display_name":"Nanjing University of Posts and Telecommunications","ror":"https://ror.org/043bpky34","country_code":"CN","type":"education","lineage":["https://openalex.org/I41198531"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shidi Tang","raw_affiliation_strings":["School of Geographic and Biological Information, Nanjing University of Posts and Telecommunications, Nanjing, China"],"raw_orcid":"https://orcid.org/0000-0001-5493-7411","affiliations":[{"raw_affiliation_string":"School of Geographic and Biological Information, Nanjing University of Posts and Telecommunications, Nanjing, China","institution_ids":["https://openalex.org/I41198531"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086764407","display_name":"Ji Ding","orcid":"https://orcid.org/0000-0002-7787-6989"},"institutions":[{"id":"https://openalex.org/I41198531","display_name":"Nanjing University of Posts and Telecommunications","ror":"https://ror.org/043bpky34","country_code":"CN","type":"education","lineage":["https://openalex.org/I41198531"]},{"id":"https://openalex.org/I76569877","display_name":"Southeast University","ror":"https://ror.org/04ct4d772","country_code":"CN","type":"education","lineage":["https://openalex.org/I76569877"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ji Ding","raw_affiliation_strings":["School of Geographic and Biological Information, Nanjing University of Posts and Telecommunications, Nanjing, China","School of Integrated Circuits, Southeast University, Nanjing, China"],"raw_orcid":"https://orcid.org/0000-0002-7787-6989","affiliations":[{"raw_affiliation_string":"School of Geographic and Biological Information, Nanjing University of Posts and Telecommunications, Nanjing, China","institution_ids":["https://openalex.org/I41198531"]},{"raw_affiliation_string":"School of Integrated Circuits, Southeast University, Nanjing, China","institution_ids":["https://openalex.org/I76569877"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5109833042","display_name":"Xiangyu Zhu","orcid":null},"institutions":[{"id":"https://openalex.org/I41198531","display_name":"Nanjing University of Posts and Telecommunications","ror":"https://ror.org/043bpky34","country_code":"CN","type":"education","lineage":["https://openalex.org/I41198531"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiangyu Zhu","raw_affiliation_strings":["School of Telecommunication and Information Engineering, Nanjing University of Posts and Telecommunications, Nanjing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Telecommunication and Information Engineering, Nanjing University of Posts and Telecommunications, Nanjing, China","institution_ids":["https://openalex.org/I41198531"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100401045","display_name":"Zheng Wang","orcid":"https://orcid.org/0000-0001-6157-0662"},"institutions":[{"id":"https://openalex.org/I45928872","display_name":"Alibaba Group (China)","ror":"https://ror.org/00k642b80","country_code":"CN","type":"company","lineage":["https://openalex.org/I45928872"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zheng Wang","raw_affiliation_strings":["Alibaba Group, Beijing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Alibaba Group, Beijing, China","institution_ids":["https://openalex.org/I45928872"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100390094","display_name":"Haitao Zhao","orcid":"https://orcid.org/0000-0002-3539-3532"},"institutions":[{"id":"https://openalex.org/I41198531","display_name":"Nanjing University of Posts and Telecommunications","ror":"https://ror.org/043bpky34","country_code":"CN","type":"education","lineage":["https://openalex.org/I41198531"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Haitao Zhao","raw_affiliation_strings":["Engineering Research Center of Health Service System Based on Ubiquitous Wireless Networks, Ministry of Education, Nanjing University of Posts and Telecommunications, Nanjing, China","Engineering Research Center of Health Service System Based on Ubiquitous Wireless Networks, Nanjing University of Posts and Telecommunications, Ministry of Education, Nanjing, China"],"raw_orcid":"https://orcid.org/0000-0002-3539-3532","affiliations":[{"raw_affiliation_string":"Engineering Research Center of Health Service System Based on Ubiquitous Wireless Networks, Ministry of Education, Nanjing University of Posts and Telecommunications, Nanjing, China","institution_ids":["https://openalex.org/I41198531"]},{"raw_affiliation_string":"Engineering Research Center of Health Service System Based on Ubiquitous Wireless Networks, Nanjing University of Posts and Telecommunications, Ministry of Education, Nanjing, China","institution_ids":["https://openalex.org/I41198531"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5102847901","display_name":"Jiansheng Wu","orcid":"https://orcid.org/0000-0002-7941-9722"},"institutions":[{"id":"https://openalex.org/I41198531","display_name":"Nanjing University of Posts and Telecommunications","ror":"https://ror.org/043bpky34","country_code":"CN","type":"education","lineage":["https://openalex.org/I41198531"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jiansheng Wu","raw_affiliation_strings":["School of Computer Science, Nanjing University of Posts and Telecommunications, Nanjing, China"],"raw_orcid":"https://orcid.org/0000-0002-7941-9722","affiliations":[{"raw_affiliation_string":"School of Computer Science, Nanjing University of Posts and Telecommunications, Nanjing, China","institution_ids":["https://openalex.org/I41198531"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":12.3123,"has_fulltext":false,"cited_by_count":27,"citation_normalized_percentile":{"value":0.98703885,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"21","issue":"6","first_page":"2382","last_page":"2393"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11796","display_name":"Horticultural and Viticultural Research","score":0.9387000203132629,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11796","display_name":"Horticultural and Viticultural Research","score":0.9387000203132629,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/autodock","display_name":"AutoDock","score":0.593288779258728},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5240305066108704},{"id":"https://openalex.org/keywords/docking","display_name":"Docking (animal)","score":0.48280656337738037},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.371543824672699},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.36808156967163086},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.04868677258491516}],"concepts":[{"id":"https://openalex.org/C2780152424","wikidata":"https://www.wikidata.org/wiki/Q4826062","display_name":"AutoDock","level":4,"score":0.593288779258728},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5240305066108704},{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.48280656337738037},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.371543824672699},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.36808156967163086},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.04868677258491516},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","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/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","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":"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":"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":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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbb.2024.3467127","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2024.3467127","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:39320991","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39320991","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":"IEEE/ACM transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Affordable and clean energy","score":0.6100000143051147,"id":"https://metadata.un.org/sdg/7"}],"awards":[{"id":"https://openalex.org/G1977326333","display_name":null,"funder_award_id":"62371245","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4947787081","display_name":"\u6837\u672c\u4fe1\u606f\u4e0d\u5145\u5206\u4e0b\u9776\u5411\u672a\u77e5\u7ed3\u6784GPCRs\u7684\u914d\u4f53\u865a\u62df\u7b5b\u9009\u65b9\u6cd5\u7814\u7a76","funder_award_id":"61872198","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":29,"referenced_works":["https://openalex.org/W1571439140","https://openalex.org/W1983194490","https://openalex.org/W1985570405","https://openalex.org/W2013085020","https://openalex.org/W2033757486","https://openalex.org/W2051434435","https://openalex.org/W2081053802","https://openalex.org/W2091683542","https://openalex.org/W2096541451","https://openalex.org/W2130479394","https://openalex.org/W2134967712","https://openalex.org/W2151568819","https://openalex.org/W2152630148","https://openalex.org/W2169678694","https://openalex.org/W2178250841","https://openalex.org/W2767891136","https://openalex.org/W2807540482","https://openalex.org/W2902812092","https://openalex.org/W2947285137","https://openalex.org/W3120361527","https://openalex.org/W3168430821","https://openalex.org/W3208898778","https://openalex.org/W4200233821","https://openalex.org/W4213076913","https://openalex.org/W4223889796","https://openalex.org/W4253543241","https://openalex.org/W4280550952","https://openalex.org/W4328048996","https://openalex.org/W6846033198"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W4391375266","https://openalex.org/W2058674645","https://openalex.org/W2766845742","https://openalex.org/W1594539819","https://openalex.org/W2007257620","https://openalex.org/W2130867670","https://openalex.org/W4213038553","https://openalex.org/W1984029386","https://openalex.org/W4312202637"],"abstract_inverted_index":{"AutoDock":[0,31,41,87],"Vina":[1,42,88],"and":[2,33,43,61,84,89,102,122,159,189,207],"its":[3,44,90],"derivatives":[4,91],"have":[5],"established":[6],"themselves":[7],"as":[8],"a":[9,68,116],"prevailing":[10],"pipeline":[11],"for":[12],"virtual":[13,51,64,103,177],"screening":[14,65,104,178],"in":[15,53,63,204,212],"contemporary":[16],"drug":[17,55],"discovery.":[18],"Our":[19,193],"Vina-GPU":[20,34,76,112,172,197,216],"method":[21],"leverages":[22],"the":[23,38,47,57,81,93,108,130,143,154,164,169],"parallel":[24],"computing":[25],"power":[26],"of":[27,40,49,59,86,95,156,171],"GPUs":[28],"to":[29,98,128,140,151,215],"accelerate":[30],"Vina,":[32],"2.0":[35],"further":[36,141],"enhances":[37],"speed":[39,60,83,206],"derivatives.":[45],"Given":[46],"prevalence":[48],"large":[50],"screens":[52],"modern":[54],"discovery,":[56],"improvement":[58,211],"accuracy":[62],"has":[66],"become":[67],"longstanding":[69],"challenge.":[70],"In":[71],"this":[72],"study,":[73],"we":[74,114,135,147,174],"propose":[75],"2.1,":[77,173],"aimed":[78],"at":[79],"enhancing":[80,163],"docking":[82,101,144,165,191,205],"precision":[85],"through":[92],"integration":[94],"novel":[96,117],"algorithms":[97],"facilitate":[99],"improved":[100],"outcomes.":[105],"Building":[106],"upon":[107],"foundations":[109],"laid":[110],"by":[111],"2.0,":[113],"introduce":[115],"algorithm,":[118],"namely":[119],"Reduced":[120],"Iteration":[121],"Low":[123],"Complexity":[124],"BFGS":[125],"(RILC-BFGS),":[126],"designed":[127],"expedite":[129],"most":[131],"time-consuming":[132],"operation.":[133],"Additionally,":[134],"implement":[136],"grid":[137],"cache":[138],"optimization":[139],"enhance":[142],"speed.":[145],"Furthermore,":[146],"employ":[148],"optimal":[149],"strategies":[150],"individually":[152],"optimize":[153],"structures":[155],"ligands,":[157],"receptors,":[158],"binding":[160],"pockets,":[161],"thereby":[162],"precision.":[166],"To":[167],"assess":[168],"performance":[170],"conduct":[175],"extensive":[176],"experiments":[179],"on":[180],"three":[181],"prominent":[182],"targets,":[183],"utilizing":[184],"two":[185],"fundamental":[186],"compound":[187],"libraries":[188],"seven":[190],"tools.":[192],"results":[194],"demonstrate":[195],"that":[196],"2.1":[198],"achieves":[199],"an":[200,208],"average":[201,209],"4.97-fold":[202],"acceleration":[203],"342%":[210],"EF1%":[213],"compared":[214],"2.0.":[217]},"counts_by_year":[{"year":2026,"cited_by_count":16},{"year":2025,"cited_by_count":10},{"year":2024,"cited_by_count":1}],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2025-10-10T00:00:00"}