{"id":"https://openalex.org/W4212886242","doi":"https://doi.org/10.1093/bioinformatics/btac120","title":"TRScore: a 3D RepVGG-based scoring method for ranking protein docking models","display_name":"TRScore: a 3D RepVGG-based scoring method for ranking protein docking models","publication_year":2022,"publication_date":"2022-02-21","ids":{"openalex":"https://openalex.org/W4212886242","doi":"https://doi.org/10.1093/bioinformatics/btac120","pmid":"https://pubmed.ncbi.nlm.nih.gov/35199137"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btac120","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac120","pdf_url":null,"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5015234704","display_name":"Linyuan Guo","orcid":null},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Linyuan Guo","raw_affiliation_strings":["Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, Hunan 410083, P.R. China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, Hunan 410083, P.R. China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059824731","display_name":"Jiahua He","orcid":"https://orcid.org/0000-0002-9075-4978"},"institutions":[{"id":"https://openalex.org/I47720641","display_name":"Huazhong University of Science and Technology","ror":"https://ror.org/00p991c53","country_code":"CN","type":"education","lineage":["https://openalex.org/I47720641"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jiahua He","raw_affiliation_strings":["School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P.R. China"],"raw_orcid":"https://orcid.org/0000-0002-9075-4978","affiliations":[{"raw_affiliation_string":"School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P.R. China","institution_ids":["https://openalex.org/I47720641"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037535665","display_name":"Peicong Lin","orcid":null},"institutions":[{"id":"https://openalex.org/I47720641","display_name":"Huazhong University of Science and Technology","ror":"https://ror.org/00p991c53","country_code":"CN","type":"education","lineage":["https://openalex.org/I47720641"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Peicong Lin","raw_affiliation_strings":["School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P.R. China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P.R. China","institution_ids":["https://openalex.org/I47720641"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053305024","display_name":"Sheng\u2010You Huang","orcid":"https://orcid.org/0000-0002-4209-4565"},"institutions":[{"id":"https://openalex.org/I47720641","display_name":"Huazhong University of Science and Technology","ror":"https://ror.org/00p991c53","country_code":"CN","type":"education","lineage":["https://openalex.org/I47720641"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Sheng-You Huang","raw_affiliation_strings":["School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P.R. China"],"raw_orcid":"https://orcid.org/0000-0002-4209-4565","affiliations":[{"raw_affiliation_string":"School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P.R. China","institution_ids":["https://openalex.org/I47720641"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100438360","display_name":"Jianxin Wang","orcid":"https://orcid.org/0000-0003-1516-0480"},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Jianxin Wang","raw_affiliation_strings":["Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, Hunan 410083, P.R. China"],"raw_orcid":"https://orcid.org/0000-0003-1516-0480","affiliations":[{"raw_affiliation_string":"Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, Hunan 410083, P.R. China","institution_ids":["https://openalex.org/I139660479"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5053305024","https://openalex.org/A5100438360"],"corresponding_institution_ids":["https://openalex.org/I139660479","https://openalex.org/I47720641"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":2.5082,"has_fulltext":false,"cited_by_count":22,"citation_normalized_percentile":{"value":0.9034257,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":99},"biblio":{"volume":"38","issue":"9","first_page":"2444","last_page":"2451"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.4596000015735626,"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":0.4596000015735626,"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":0.19130000472068787,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.1501999944448471,"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":0.7800215482711792},{"id":"https://openalex.org/keywords/ranking","display_name":"Ranking (information retrieval)","score":0.6794987916946411},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6533387899398804},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4119432270526886},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3963565528392792},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.37657299637794495},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3508051037788391},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1313619315624237},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.06439778208732605}],"concepts":[{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.7800215482711792},{"id":"https://openalex.org/C189430467","wikidata":"https://www.wikidata.org/wiki/Q7293293","display_name":"Ranking (information retrieval)","level":2,"score":0.6794987916946411},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6533387899398804},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4119432270526886},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3963565528392792},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.37657299637794495},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3508051037788391},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1313619315624237},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.06439778208732605},{"id":"https://openalex.org/C159110408","wikidata":"https://www.wikidata.org/wiki/Q121176","display_name":"Nursing","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","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":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D012107","descriptor_name":"Research Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012107","descriptor_name":"Research Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012107","descriptor_name":"Research Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053246","descriptor_name":"Receptor Activator of Nuclear Factor-kappa B","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D053246","descriptor_name":"Receptor Activator of Nuclear Factor-kappa B","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D053246","descriptor_name":"Receptor Activator of Nuclear Factor-kappa B","qualifier_ui":"Q000378","qualifier_name":"metabolism","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},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btac120","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac120","pdf_url":null,"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:35199137","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35199137","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}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1377489580","display_name":null,"funder_award_id":"32161133002","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G1729077721","display_name":null,"funder_award_id":"61732009","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3310655903","display_name":null,"funder_award_id":"62072199","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4043378463","display_name":null,"funder_award_id":"61832019","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G611205877","display_name":null,"funder_award_id":"2021YFF1201200","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":62,"referenced_works":["https://openalex.org/W174644880","https://openalex.org/W1030883578","https://openalex.org/W1724277458","https://openalex.org/W1979284950","https://openalex.org/W1993951624","https://openalex.org/W2000383223","https://openalex.org/W2005303195","https://openalex.org/W2054394841","https://openalex.org/W2073911195","https://openalex.org/W2090672363","https://openalex.org/W2105572387","https://openalex.org/W2111387452","https://openalex.org/W2114194071","https://openalex.org/W2118514515","https://openalex.org/W2119333768","https://openalex.org/W2124981562","https://openalex.org/W2128900650","https://openalex.org/W2129454543","https://openalex.org/W2133712572","https://openalex.org/W2139281871","https://openalex.org/W2145793759","https://openalex.org/W2153983456","https://openalex.org/W2157991822","https://openalex.org/W2163605009","https://openalex.org/W2204887665","https://openalex.org/W2252854990","https://openalex.org/W2315317366","https://openalex.org/W2329592726","https://openalex.org/W2420141398","https://openalex.org/W2465190302","https://openalex.org/W2508425869","https://openalex.org/W2572080171","https://openalex.org/W2583907533","https://openalex.org/W2625768267","https://openalex.org/W2766246727","https://openalex.org/W2767509030","https://openalex.org/W2784213390","https://openalex.org/W2799682268","https://openalex.org/W2808950571","https://openalex.org/W2890911678","https://openalex.org/W2912457464","https://openalex.org/W2912460249","https://openalex.org/W2915344963","https://openalex.org/W2950365860","https://openalex.org/W2951646940","https://openalex.org/W2956081200","https://openalex.org/W2971405760","https://openalex.org/W2980678340","https://openalex.org/W2990594531","https://openalex.org/W2990689232","https://openalex.org/W2992752586","https://openalex.org/W2999044305","https://openalex.org/W3014616217","https://openalex.org/W3015438624","https://openalex.org/W3081249922","https://openalex.org/W3096136978","https://openalex.org/W3129073614","https://openalex.org/W3133540795","https://openalex.org/W3133793061","https://openalex.org/W3195593976","https://openalex.org/W4233587745","https://openalex.org/W6684191040"],"related_works":["https://openalex.org/W2188500270","https://openalex.org/W2303858293","https://openalex.org/W2915512527","https://openalex.org/W2798198862","https://openalex.org/W51364034","https://openalex.org/W2798997222","https://openalex.org/W2793336762","https://openalex.org/W2091548507","https://openalex.org/W2575434942","https://openalex.org/W2047838177"],"abstract_inverted_index":{"MOTIVATION:":[0],"Protein-protein":[1],"interactions":[2],"(PPI)":[3],"play":[4],"important":[5,42],"roles":[6],"in":[7,46,75,126,191],"cellular":[8],"activities.":[9],"Due":[10],"to":[11,35],"the":[12,26,41,113,122,132,141],"technical":[13],"difficulty":[14],"and":[15,43,149,182,193],"high":[16],"cost":[17],"of":[18,28,40,56,109,124],"experimental":[19],"methods,":[20],"there":[21],"are":[22,72],"considerable":[23],"interests":[24],"towards":[25],"development":[27],"computational":[29],"approaches,":[30],"such":[31],"as":[32,175,177],"protein":[33,47],"docking,":[34],"decipher":[36],"PPI":[37],"patterns.":[38],"One":[39],"difficult":[44],"aspects":[45],"docking":[48,92,167],"is":[49],"recognizing":[50],"near-native":[51,104,147],"conformations":[52,105],"from":[53,65,106,131],"a":[54,83,96,107,117,185],"set":[55,108,181],"decoys,":[57,110],"but":[58],"unfortunately,":[59],"traditional":[60],"scoring":[61,70,87],"functions":[62],"still":[63],"suffer":[64],"limited":[66],"accuracy.":[67],"Therefore,":[68],"new":[69,84],"methods":[71,190],"pressingly":[73],"needed":[74],"methodological":[76],"and/or":[77],"practical":[78],"implications.":[79],"RESULTS:":[80],"We":[81],"present":[82],"deep":[85,133],"learning-based":[86],"method":[88],"for":[89],"ranking":[90],"protein-protein":[91,114,166],"models":[93,148],"based":[94],"on":[95,161],"3D":[97,118],"RepVGG":[98,135],"network,":[99],"named":[100],"TRScore.":[101],"To":[102],"recognize":[103],"TRScore":[111,137,157],"voxelizes":[112],"interface":[115],"into":[116],"grid":[119],"labeled":[120],"by":[121],"number":[123],"atoms":[125],"different":[127],"physicochemical":[128],"classes.":[129],"Benefiting":[130],"convolutional":[134],"architecture,":[136],"can":[138],"effectively":[139],"capture":[140],"subtle":[142],"differences":[143],"between":[144],"energetically":[145],"favorable":[146],"unfavorable":[150],"non-native":[151],"decoys":[152],"without":[153],"needing":[154],"extra":[155],"information.":[156],"was":[158],"extensively":[159],"evaluated":[160],"diverse":[162],"test":[163],"sets":[164],"including":[165],"benchmark":[168],"5.0":[169],"update":[170],"set,":[171,174],"DockGround":[172],"decoy":[173,180],"well":[176],"realistic":[178],"CAPRI":[179],"overall":[183],"obtained":[184],"significant":[186],"improvement":[187],"over":[188],"existing":[189],"cross-validation":[192],"independent":[194],"evaluations.":[195],"AVAILABILITY":[196],"AND":[197],"IMPLEMENTATION:":[198],"Codes":[199],"available":[200],"at:":[201],"https://github.com/BioinformaticsCSU/TRScore.":[202]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":8},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":6}],"updated_date":"2026-08-18T07:49:30.821534","created_date":"2025-10-10T00:00:00"}
