{"id":"https://openalex.org/W4319999782","doi":"https://doi.org/10.1109/jbhi.2023.3240305","title":"Predicting Drug-Target Affinity by Learning Protein Knowledge From Biological Networks","display_name":"Predicting Drug-Target Affinity by Learning Protein Knowledge From Biological Networks","publication_year":2023,"publication_date":"2023-01-27","ids":{"openalex":"https://openalex.org/W4319999782","doi":"https://doi.org/10.1109/jbhi.2023.3240305","pmid":"https://pubmed.ncbi.nlm.nih.gov/37018115"},"language":"en","primary_location":{"id":"doi:10.1109/jbhi.2023.3240305","is_oa":false,"landing_page_url":"https://doi.org/10.1109/jbhi.2023.3240305","pdf_url":null,"source":{"id":"https://openalex.org/S2495854775","display_name":"IEEE Journal of Biomedical and Health Informatics","issn_l":"2168-2194","issn":["2168-2194","2168-2208"],"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 Journal of Biomedical and Health Informatics","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/A5083382988","display_name":"Wenjian Ma","orcid":"https://orcid.org/0000-0001-8725-1029"},"institutions":[{"id":"https://openalex.org/I59028903","display_name":"Ocean University of China","ror":"https://ror.org/04rdtx186","country_code":"CN","type":"education","lineage":["https://openalex.org/I59028903"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Wenjian Ma","raw_affiliation_strings":["College of Computer Science and Technology, Ocean University of China, Qingdao, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, Ocean University of China, Qingdao, China","institution_ids":["https://openalex.org/I59028903"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101822148","display_name":"Shugang Zhang","orcid":"https://orcid.org/0000-0002-9774-9709"},"institutions":[{"id":"https://openalex.org/I59028903","display_name":"Ocean University of China","ror":"https://ror.org/04rdtx186","country_code":"CN","type":"education","lineage":["https://openalex.org/I59028903"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shugang Zhang","raw_affiliation_strings":["College of Computer Science and Technology, Ocean University of China, Qingdao, China"],"raw_orcid":"https://orcid.org/0000-0002-9774-9709","affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, Ocean University of China, Qingdao, China","institution_ids":["https://openalex.org/I59028903"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100680995","display_name":"Zhen Li","orcid":"https://orcid.org/0000-0001-5093-4221"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Zhen Li","raw_affiliation_strings":["College of Computer Science and Technology, Qingdao University, Qingdao, China"],"raw_orcid":"https://orcid.org/0000-0001-5093-4221","affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, Qingdao University, Qingdao, China","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076937227","display_name":"Mingjian Jiang","orcid":"https://orcid.org/0000-0002-0716-5292"},"institutions":[{"id":"https://openalex.org/I44468530","display_name":"Qingdao University of Technology","ror":"https://ror.org/01qzc0f54","country_code":"CN","type":"education","lineage":["https://openalex.org/I44468530"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Mingjian Jiang","raw_affiliation_strings":["School of Information and Control Engineering, Qingdao University of Technology, Qingdao, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Information and Control Engineering, Qingdao University of Technology, Qingdao, China","institution_ids":["https://openalex.org/I44468530"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100375587","display_name":"Shuang Wang","orcid":"https://orcid.org/0000-0002-6779-9537"},"institutions":[{"id":"https://openalex.org/I4210162190","display_name":"China University of Petroleum, East China","ror":"https://ror.org/05gbn2817","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210162190"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shuang Wang","raw_affiliation_strings":["College of Computer Science and Technology, China University of Petroleum (East China), Qingdao, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, China University of Petroleum (East China), Qingdao, China","institution_ids":["https://openalex.org/I4210162190"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005922830","display_name":"Nianfan Guo","orcid":null},"institutions":[{"id":"https://openalex.org/I59028903","display_name":"Ocean University of China","ror":"https://ror.org/04rdtx186","country_code":"CN","type":"education","lineage":["https://openalex.org/I59028903"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Nianfan Guo","raw_affiliation_strings":["College of Computer Science and Technology, Ocean University of China, Qingdao, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, Ocean University of China, Qingdao, China","institution_ids":["https://openalex.org/I59028903"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101472325","display_name":"Yuanfei Li","orcid":"https://orcid.org/0000-0002-9314-4104"},"institutions":[{"id":"https://openalex.org/I59028903","display_name":"Ocean University of China","ror":"https://ror.org/04rdtx186","country_code":"CN","type":"education","lineage":["https://openalex.org/I59028903"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yuanfei Li","raw_affiliation_strings":["College of Computer Science and Technology, Ocean University of China, Qingdao, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, Ocean University of China, Qingdao, China","institution_ids":["https://openalex.org/I59028903"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075836788","display_name":"Xiangpeng Bi","orcid":"https://orcid.org/0000-0003-4712-0870"},"institutions":[{"id":"https://openalex.org/I59028903","display_name":"Ocean University of China","ror":"https://ror.org/04rdtx186","country_code":"CN","type":"education","lineage":["https://openalex.org/I59028903"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiangpeng Bi","raw_affiliation_strings":["College of Computer Science and Technology, Ocean University of China, Qingdao, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, Ocean University of China, Qingdao, China","institution_ids":["https://openalex.org/I59028903"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032230008","display_name":"Huasen Jiang","orcid":"https://orcid.org/0000-0001-6802-1017"},"institutions":[{"id":"https://openalex.org/I59028903","display_name":"Ocean University of China","ror":"https://ror.org/04rdtx186","country_code":"CN","type":"education","lineage":["https://openalex.org/I59028903"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Huasen Jiang","raw_affiliation_strings":["College of Computer Science and Technology, Ocean University of China, Qingdao, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, Ocean University of China, Qingdao, China","institution_ids":["https://openalex.org/I59028903"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5079932099","display_name":"Zhiqiang Wei","orcid":"https://orcid.org/0000-0002-2830-8301"},"institutions":[{"id":"https://openalex.org/I59028903","display_name":"Ocean University of China","ror":"https://ror.org/04rdtx186","country_code":"CN","type":"education","lineage":["https://openalex.org/I59028903"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhiqiang Wei","raw_affiliation_strings":["College of Computer Science and Technology, Ocean University of China, Qingdao, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, Ocean University of China, Qingdao, China","institution_ids":["https://openalex.org/I59028903"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":10,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":7.6375,"has_fulltext":false,"cited_by_count":41,"citation_normalized_percentile":{"value":0.97831879,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":100},"biblio":{"volume":"27","issue":"4","first_page":"2128","last_page":"2137"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9998999834060669,"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":0.9998999834060669,"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":0.9973999857902527,"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":0.9958000183105469,"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":0.5163989663124084},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5110126733779907},{"id":"https://openalex.org/keywords/drug-target","display_name":"Drug target","score":0.44003331661224365},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3239838778972626},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.186754047870636},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.09461858868598938}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5163989663124084},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5110126733779907},{"id":"https://openalex.org/C2989108626","wikidata":"https://www.wikidata.org/wiki/Q904407","display_name":"Drug target","level":2,"score":0.44003331661224365},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3239838778972626},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.186754047870636},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.09461858868598938}],"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":"D019359","descriptor_name":"Knowledge","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019359","descriptor_name":"Knowledge","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019359","descriptor_name":"Knowledge","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1109/jbhi.2023.3240305","is_oa":false,"landing_page_url":"https://doi.org/10.1109/jbhi.2023.3240305","pdf_url":null,"source":{"id":"https://openalex.org/S2495854775","display_name":"IEEE Journal of Biomedical and Health Informatics","issn_l":"2168-2194","issn":["2168-2194","2168-2208"],"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 Journal of Biomedical and Health Informatics","raw_type":"journal-article"},{"id":"pmid:37018115","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37018115","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 journal of biomedical and health informatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3","score":0.47999998927116394}],"awards":[],"funders":[{"id":"https://openalex.org/F4320335787","display_name":"Fundamental Research Funds for the Central Universities","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":52,"referenced_works":["https://openalex.org/W1971650367","https://openalex.org/W1975147762","https://openalex.org/W1982267716","https://openalex.org/W1998931368","https://openalex.org/W2033178790","https://openalex.org/W2035585923","https://openalex.org/W2036696353","https://openalex.org/W2086286404","https://openalex.org/W2101181377","https://openalex.org/W2116341502","https://openalex.org/W2148145769","https://openalex.org/W2155744824","https://openalex.org/W2158714788","https://openalex.org/W2168223461","https://openalex.org/W2523246573","https://openalex.org/W2605952223","https://openalex.org/W2744129621","https://openalex.org/W2767891136","https://openalex.org/W2785947426","https://openalex.org/W2807704635","https://openalex.org/W2808199968","https://openalex.org/W2809216727","https://openalex.org/W2860192827","https://openalex.org/W2911871527","https://openalex.org/W2971801381","https://openalex.org/W2996367417","https://openalex.org/W3004604833","https://openalex.org/W3005769002","https://openalex.org/W3006973065","https://openalex.org/W3016077459","https://openalex.org/W3028589594","https://openalex.org/W3032123378","https://openalex.org/W3038467106","https://openalex.org/W3047995329","https://openalex.org/W3094967361","https://openalex.org/W3095583226","https://openalex.org/W3096561213","https://openalex.org/W3107527779","https://openalex.org/W3112376646","https://openalex.org/W3117081956","https://openalex.org/W3123943527","https://openalex.org/W3133246485","https://openalex.org/W3152870288","https://openalex.org/W3187647935","https://openalex.org/W4205167309","https://openalex.org/W4207030893","https://openalex.org/W4297179162","https://openalex.org/W6716936834","https://openalex.org/W6726873649","https://openalex.org/W6727249380","https://openalex.org/W6766978945","https://openalex.org/W6775123410"],"related_works":["https://openalex.org/W2961085424","https://openalex.org/W4306674287","https://openalex.org/W4224009465","https://openalex.org/W4286629047","https://openalex.org/W4306321456","https://openalex.org/W4285260836","https://openalex.org/W3046775127","https://openalex.org/W3170094116","https://openalex.org/W4205958290","https://openalex.org/W4386462264"],"abstract_inverted_index":{"Predicting":[0],"drug-target":[1],"affinity":[2],"(DTA)":[3],"is":[4],"a":[5,38,128,142,201],"crucial":[6],"step":[7],"in":[8,95,159],"the":[9,23,35,50,74,78,83,100,138,150,175,207,218],"process":[10],"of":[11,18,28,37,41,49,52,77,135,141],"drug":[12,30],"discovery.":[13],"Efficient":[14],"and":[15,25,63,164,205,222],"accurate":[16],"prediction":[17,45,109,210,220],"DTA":[19,44,108,209,219],"would":[20],"greatly":[21],"reduce":[22],"time":[24],"economic":[26],"cost":[27],"new":[29,215],"development,":[31],"which":[32,186],"has":[33],"encouraged":[34],"emergence":[36],"large":[39],"number":[40],"deep":[42],"learning-based":[43],"methods.":[46,66,235],"In":[47],"terms":[48],"representation":[51,176,204],"target":[53,79,143,151],"proteins,":[54],"current":[55,233],"methods":[56],"can":[57,120],"be":[58,121],"classified":[59],"into":[60],"1D":[61],"sequence-":[62],"2D-protein":[64],"graph-based":[65],"However,":[67],"both":[68],"two":[69],"approaches":[70],"focused":[71],"only":[72,137,189],"on":[73],"inherent":[75,139],"properties":[76],"protein,":[80,144],"but":[81,193],"neglected":[82],"broad":[84],"prior":[85,172],"knowledge":[86],"regarding":[87],"protein":[88,132,152,203],"interactions":[89],"that":[90,226],"have":[91],"been":[92],"clearly":[93],"elucidated":[94],"past":[96],"decades.":[97],"Aiming":[98],"at":[99],"above":[101],"issue,":[102],"this":[103],"work":[104],"presents":[105],"an":[106,180],"end-to-end":[107],"method":[110],"named":[111],"MSF-DTA":[112,126,145,227],"(Multi-Source":[113],"Feature":[114],"Fusion-based":[115],"Drug-Target":[116],"Affinity).":[117],"The":[118],"contributions":[119],"summarized":[122],"as":[123],"follows.":[124],"First,":[125],"adopts":[127],"novel":[129],"\"neighboring":[130],"feature\"-based":[131],"representation.":[133],"Instead":[134],"utilizing":[136],"features":[140,192],"gathers":[146],"additional":[147],"information":[148],"for":[149,217],"from":[153],"its":[154],"biologically":[155],"related":[156],"\"neighboring\"":[157],"proteins":[158],"PPI":[160],"(i.e.,":[161,166],"protein-protein":[162],"interaction)":[163],"SSN":[165],"sequence":[167],"similarity)":[168],"networks":[169],"to":[170,200,232],"get":[171],"knowledge.":[173],"Second,":[174],"was":[177],"learned":[178],"using":[179],"advanced":[181],"graph":[182],"pre-training":[183],"framework,":[184],"VGAE,":[185],"could":[187],"not":[188],"gather":[190],"node":[191],"also":[194],"learn":[195],"topological":[196],"connections,":[197],"therefore":[198],"contributing":[199],"richer":[202],"benefiting":[206],"downstream":[208],"task.":[211],"This":[212],"study":[213],"provides":[214],"perspective":[216],"task,":[221],"evaluation":[223],"results":[224],"demonstrated":[225],"obtained":[228],"superior":[229],"performances":[230],"compared":[231],"state-of-the-art":[234]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":18},{"year":2024,"cited_by_count":13},{"year":2023,"cited_by_count":5}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
