{"id":"https://openalex.org/W7127046274","doi":"https://doi.org/10.1186/s12859-026-06377-4","title":"Contrastive learning in both structure and function spaces improve drug-target interaction prediction","display_name":"Contrastive learning in both structure and function spaces improve drug-target interaction prediction","publication_year":2026,"publication_date":"2026-02-02","ids":{"openalex":"https://openalex.org/W7127046274","doi":"https://doi.org/10.1186/s12859-026-06377-4","pmid":"https://pubmed.ncbi.nlm.nih.gov/41629789"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-026-06377-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-026-06377-4","pdf_url":null,"source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1186/s12859-026-06377-4","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5124741105","display_name":"Yongqing Zhang","orcid":null},"institutions":[{"id":"https://openalex.org/I24201400","display_name":"Chengdu University of Information Technology","ror":"https://ror.org/01yxwrh59","country_code":"CN","type":"education","lineage":["https://openalex.org/I24201400"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yongqing Zhang","raw_affiliation_strings":["Chengdu University of Information Technology, Chengdu, 610225, China"],"affiliations":[{"raw_affiliation_string":"Chengdu University of Information Technology, Chengdu, 610225, China","institution_ids":["https://openalex.org/I24201400"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5124698076","display_name":"Le Chen","orcid":null},"institutions":[{"id":"https://openalex.org/I24201400","display_name":"Chengdu University of Information Technology","ror":"https://ror.org/01yxwrh59","country_code":"CN","type":"education","lineage":["https://openalex.org/I24201400"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Le Chen","raw_affiliation_strings":["Chengdu University of Information Technology, Chengdu, 610225, China"],"affiliations":[{"raw_affiliation_string":"Chengdu University of Information Technology, Chengdu, 610225, China","institution_ids":["https://openalex.org/I24201400"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5124696632","display_name":"Hong Luo","orcid":null},"institutions":[{"id":"https://openalex.org/I24201400","display_name":"Chengdu University of Information Technology","ror":"https://ror.org/01yxwrh59","country_code":"CN","type":"education","lineage":["https://openalex.org/I24201400"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hong Luo","raw_affiliation_strings":["Chengdu University of Information Technology, Chengdu, 610225, China"],"affiliations":[{"raw_affiliation_string":"Chengdu University of Information Technology, Chengdu, 610225, China","institution_ids":["https://openalex.org/I24201400"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5124730886","display_name":"Tianhao Li","orcid":null},"institutions":[{"id":"https://openalex.org/I24201400","display_name":"Chengdu University of Information Technology","ror":"https://ror.org/01yxwrh59","country_code":"CN","type":"education","lineage":["https://openalex.org/I24201400"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Tianhao Li","raw_affiliation_strings":["Chengdu University of Information Technology, Chengdu, 610225, China"],"affiliations":[{"raw_affiliation_string":"Chengdu University of Information Technology, Chengdu, 610225, China","institution_ids":["https://openalex.org/I24201400"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5124705900","display_name":"Shuwen Xiong","orcid":null},"institutions":[{"id":"https://openalex.org/I24201400","display_name":"Chengdu University of Information Technology","ror":"https://ror.org/01yxwrh59","country_code":"CN","type":"education","lineage":["https://openalex.org/I24201400"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shuwen Xiong","raw_affiliation_strings":["Chengdu University of Information Technology, Chengdu, 610225, China"],"affiliations":[{"raw_affiliation_string":"Chengdu University of Information Technology, Chengdu, 610225, China","institution_ids":["https://openalex.org/I24201400"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5124711669","display_name":"Zixuan Wang","orcid":null},"institutions":[{"id":"https://openalex.org/I24185976","display_name":"Sichuan University","ror":"https://ror.org/011ashp19","country_code":"CN","type":"education","lineage":["https://openalex.org/I24185976"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zixuan Wang","raw_affiliation_strings":["Sichuan University, Chengdu, 610065, China"],"affiliations":[{"raw_affiliation_string":"Sichuan University, Chengdu, 610065, China","institution_ids":["https://openalex.org/I24185976"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5124749250","display_name":"Quan Zou","orcid":null},"institutions":[{"id":"https://openalex.org/I150229711","display_name":"University of Electronic Science and Technology of China","ror":"https://ror.org/04qr3zq92","country_code":"CN","type":"education","lineage":["https://openalex.org/I150229711"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Quan Zou","raw_affiliation_strings":["University of Electronic Science and Technology of China, Chengdu, 611731, China"],"affiliations":[{"raw_affiliation_string":"University of Electronic Science and Technology of China, Chengdu, 611731, China","institution_ids":["https://openalex.org/I150229711"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5124740531","display_name":"Wenqian Zhang","orcid":null},"institutions":[{"id":"https://openalex.org/I2800232565","display_name":"Beijing Chao-Yang Hospital, Capital Medical University","ror":"https://ror.org/01eff5662","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I2800232565","https://openalex.org/I4210110145","https://openalex.org/I4210135108"]},{"id":"https://openalex.org/I4210164898","display_name":"Beijing Chaoyang Emergency Medical Center","ror":"https://ror.org/05anb7a53","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210164898"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Wenqian Zhang","raw_affiliation_strings":["Department of Thoracic Surgery, Beijing Chaoyang Hospital, Capital Medical University, Beijing, 100020, China. wenqian.zhang@hotmail.com"],"affiliations":[{"raw_affiliation_string":"Department of Thoracic Surgery, Beijing Chaoyang Hospital, Capital Medical University, Beijing, 100020, China. wenqian.zhang@hotmail.com","institution_ids":["https://openalex.org/I2800232565","https://openalex.org/I4210164898"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5124740531"],"corresponding_institution_ids":["https://openalex.org/I2800232565","https://openalex.org/I4210164898"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.25111531,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"27","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9822999835014343,"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":0.9822999835014343,"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":0.00430000014603138,"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/T11948","display_name":"Machine Learning in Materials Science","score":0.002300000051036477,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/generalization","display_name":"Generalization","score":0.7486000061035156},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.6534000039100647},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.5346999764442444},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.47269999980926514},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.4471000134944916},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.41780000925064087},{"id":"https://openalex.org/keywords/feature-extraction","display_name":"Feature extraction","score":0.3391999900341034},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.3262999951839447}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7822999954223633},{"id":"https://openalex.org/C177148314","wikidata":"https://www.wikidata.org/wiki/Q170084","display_name":"Generalization","level":2,"score":0.7486000061035156},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.6534000039100647},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.645799994468689},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5597000122070312},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.5346999764442444},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.47269999980926514},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.4471000134944916},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.41780000925064087},{"id":"https://openalex.org/C52622490","wikidata":"https://www.wikidata.org/wiki/Q1026626","display_name":"Feature extraction","level":2,"score":0.3391999900341034},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.3262999951839447},{"id":"https://openalex.org/C59404180","wikidata":"https://www.wikidata.org/wiki/Q17013334","display_name":"Feature learning","level":2,"score":0.3239000141620636},{"id":"https://openalex.org/C2989108626","wikidata":"https://www.wikidata.org/wiki/Q904407","display_name":"Drug target","level":2,"score":0.3206000030040741},{"id":"https://openalex.org/C66024118","wikidata":"https://www.wikidata.org/wiki/Q1122506","display_name":"Computational model","level":2,"score":0.3174000084400177},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3125},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.295199990272522},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.28459998965263367},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.28130000829696655},{"id":"https://openalex.org/C94124525","wikidata":"https://www.wikidata.org/wiki/Q912550","display_name":"Categorization","level":2,"score":0.2809000015258789},{"id":"https://openalex.org/C83665646","wikidata":"https://www.wikidata.org/wiki/Q42139305","display_name":"Feature vector","level":2,"score":0.2775999903678894},{"id":"https://openalex.org/C22367795","wikidata":"https://www.wikidata.org/wiki/Q7625208","display_name":"Structured prediction","level":2,"score":0.2728999853134155},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.2635999917984009},{"id":"https://openalex.org/C2775941552","wikidata":"https://www.wikidata.org/wiki/Q25212305","display_name":"Isolation (microbiology)","level":2,"score":0.25459998846054077},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.25049999356269836}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-026-06377-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-026-06377-4","pdf_url":null,"source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:41629789","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41629789","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:bd0f4158a43e4948aea2cc5463b6da5e","is_oa":true,"landing_page_url":"https://doaj.org/article/bd0f4158a43e4948aea2cc5463b6da5e","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 27, Iss 1 (2026)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12951913","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12951913/","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-026-06377-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-026-06377-4","pdf_url":null,"source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G8617958116","display_name":null,"funder_award_id":"62272067","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":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":45,"referenced_works":["https://openalex.org/W1995887851","https://openalex.org/W2015982647","https://openalex.org/W2035585923","https://openalex.org/W2080642200","https://openalex.org/W2096541451","https://openalex.org/W2100257305","https://openalex.org/W2108069034","https://openalex.org/W2128049108","https://openalex.org/W2135007932","https://openalex.org/W2139736926","https://openalex.org/W2153838454","https://openalex.org/W2165674132","https://openalex.org/W2170146596","https://openalex.org/W2192682263","https://openalex.org/W2200017991","https://openalex.org/W2412446857","https://openalex.org/W2513544049","https://openalex.org/W2553681302","https://openalex.org/W2899788782","https://openalex.org/W2904742480","https://openalex.org/W2982499649","https://openalex.org/W3006737593","https://openalex.org/W3018980093","https://openalex.org/W3021338900","https://openalex.org/W3028589594","https://openalex.org/W3082081167","https://openalex.org/W3126516421","https://openalex.org/W3136918052","https://openalex.org/W3192677404","https://openalex.org/W3201055938","https://openalex.org/W3206585172","https://openalex.org/W3209981042","https://openalex.org/W3215525389","https://openalex.org/W4206078729","https://openalex.org/W4292723103","https://openalex.org/W4296162381","https://openalex.org/W4306292879","https://openalex.org/W4307178567","https://openalex.org/W4313423934","https://openalex.org/W4323653718","https://openalex.org/W4386046819","https://openalex.org/W4402592508","https://openalex.org/W4403782367","https://openalex.org/W4404101355","https://openalex.org/W4412203731"],"related_works":[],"abstract_inverted_index":{"Identifying":[0],"drug\u2013target":[1],"interactions":[2,37],"(DTIs)":[3],"is":[4],"essential":[5],"in":[6,143,165,188],"drug":[7,65,144],"discovery":[8],"and":[9,60,66,127,158,169,180,193],"repositioning.":[10],"Recently,":[11],"deep":[12],"learning":[13,71,152],"has":[14,29,170],"become":[15],"the":[16,23,64,73,80,105,120,124,139,175,189],"mainstream":[17],"methodology":[18],"for":[19,138],"DTI":[20],"prediction.":[21],"However,":[22,174],"scarcity":[24],"of":[25,130,177],"three-dimensional":[26],"structural":[27,59,157],"data":[28,179,192],"forced":[30],"almost":[31],"all":[32],"methods":[33,164],"to":[34,90,185],"predict":[35],"drug-target":[36,166],"with":[38],"low-dimensional":[39],"data,":[40],"thereby":[41],"constraining":[42],"their":[43],"overall":[44,107],"performance.":[45],"In":[46],"tackling":[47],"this":[48],"challenge,":[49],"we":[50,116],"introduce":[51],"a":[52,91,150],"novel":[53],"approach,":[54],"CLSF-DTI.":[55,131],"CLSF-DTI":[56,103,133,154],"incorporates":[57],"high-dimensional":[58],"functional":[61,159],"information":[62],"into":[63],"protein":[67,140],"features":[68],"through":[69],"contrastive":[70,121,151],"during":[72],"feature":[74],"extraction":[75],"stage.":[76],"This":[77,147],"ensures":[78],"that":[79,102,119,155],"model":[81,153],"no":[82],"longer":[83],"solely":[84],"focuses":[85],"on":[86,97],"sequence":[87],"information,":[88],"leading":[89],"more":[92],"precise":[93],"modeling":[94],"outcome.":[95],"Experiments":[96],"five":[98,110],"benchmark":[99],"datasets":[100],"demonstrate":[101],"achieves":[104],"best":[106],"performance":[108,126],"among":[109],"state-of-the-art":[111],"baselines.":[112],"Through":[113],"ablation":[114],"studies,":[115],"further":[117],"prove":[118],"module":[122],"enhances":[123],"predictive":[125],"generalization":[128,172],"ability":[129],"Moreover,":[132],"successfully":[134],"identified":[135],"some":[136],"ligands":[137],"PKA-C$$\\alpha":[141],"$$":[142],"screening":[145],"experiments.":[146],"study":[148],"proposed":[149],"integrates":[156],"similarity.":[160],"It":[161],"outperforms":[162],"existing":[163],"interaction":[167],"prediction":[168],"stronger":[171],"ability.":[173],"handling":[176],"unbalanced":[178],"long-distance":[181],"dependencies":[182],"still":[183],"needs":[184],"be":[186],"improved":[187],"future.":[190],"The":[191],"source":[194],"code":[195],"are":[196],"available":[197],"at":[198],"https://github.com/ZhangLab312/CLSF_DTI.":[199]},"counts_by_year":[],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2026-02-03T00:00:00"}