{"id":"https://openalex.org/W4394711270","doi":"https://doi.org/10.1109/tai.2024.3387402","title":"A Unified Conditional Diffusion Framework for Dual Protein Targets-Based Bioactive Molecule Generation","display_name":"A Unified Conditional Diffusion Framework for Dual Protein Targets-Based Bioactive Molecule Generation","publication_year":2024,"publication_date":"2024-04-11","ids":{"openalex":"https://openalex.org/W4394711270","doi":"https://doi.org/10.1109/tai.2024.3387402"},"language":"en","primary_location":{"id":"doi:10.1109/tai.2024.3387402","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tai.2024.3387402","pdf_url":null,"source":{"id":"https://openalex.org/S4210169448","display_name":"IEEE Transactions on Artificial Intelligence","issn_l":"2691-4581","issn":["2691-4581"],"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 Transactions on Artificial Intelligence","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"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/A5100727472","display_name":"Lei Huang","orcid":"https://orcid.org/0000-0003-2458-5149"},"institutions":[{"id":"https://openalex.org/I168719708","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23","country_code":"HK","type":"education","lineage":["https://openalex.org/I168719708"]}],"countries":["HK"],"is_corresponding":true,"raw_author_name":"Lei Huang","raw_affiliation_strings":["Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong SAR"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong SAR","institution_ids":["https://openalex.org/I168719708"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020682113","display_name":"Zheng Yuan","orcid":"https://orcid.org/0000-0001-7179-2437"},"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 Yuan","raw_affiliation_strings":["Alibaba Damo Academy, Hangzhou, China"],"affiliations":[{"raw_affiliation_string":"Alibaba Damo Academy, Hangzhou, China","institution_ids":["https://openalex.org/I45928872"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021581145","display_name":"Huihui Yan","orcid":"https://orcid.org/0000-0002-6978-6350"},"institutions":[{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Huihui Yan","raw_affiliation_strings":["Zhejiang University, Hangzhou, China"],"affiliations":[{"raw_affiliation_string":"Zhejiang University, Hangzhou, China","institution_ids":["https://openalex.org/I76130692"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060450271","display_name":"Rong Sheng","orcid":"https://orcid.org/0000-0002-5347-431X"},"institutions":[{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Rong Sheng","raw_affiliation_strings":["Zhejiang University, Hangzhou, China"],"affiliations":[{"raw_affiliation_string":"Zhejiang University, Hangzhou, China","institution_ids":["https://openalex.org/I76130692"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032961872","display_name":"Linjing Liu","orcid":null},"institutions":[{"id":"https://openalex.org/I168719708","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23","country_code":"HK","type":"education","lineage":["https://openalex.org/I168719708"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Linjing Liu","raw_affiliation_strings":["Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong SAR"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong SAR","institution_ids":["https://openalex.org/I168719708"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101714505","display_name":"Fuzhou Wang","orcid":"https://orcid.org/0000-0002-9028-5382"},"institutions":[{"id":"https://openalex.org/I168719708","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23","country_code":"HK","type":"education","lineage":["https://openalex.org/I168719708"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Fuzhou Wang","raw_affiliation_strings":["Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong SAR"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong SAR","institution_ids":["https://openalex.org/I168719708"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062106534","display_name":"Weidun Xie","orcid":"https://orcid.org/0000-0001-9009-2647"},"institutions":[{"id":"https://openalex.org/I168719708","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23","country_code":"HK","type":"education","lineage":["https://openalex.org/I168719708"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Weidun Xie","raw_affiliation_strings":["Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong SAR"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong SAR","institution_ids":["https://openalex.org/I168719708"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101403239","display_name":"Nanjun Chen","orcid":"https://orcid.org/0000-0003-1432-3495"},"institutions":[{"id":"https://openalex.org/I168719708","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23","country_code":"HK","type":"education","lineage":["https://openalex.org/I168719708"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Nanjun Chen","raw_affiliation_strings":["Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong SAR"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong SAR","institution_ids":["https://openalex.org/I168719708"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101488344","display_name":"Fei Huang","orcid":"https://orcid.org/0000-0002-3709-5053"},"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":"Fei Huang","raw_affiliation_strings":["Alibaba Damo Academy, Hangzhou, China"],"affiliations":[{"raw_affiliation_string":"Alibaba Damo Academy, Hangzhou, China","institution_ids":["https://openalex.org/I45928872"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047856952","display_name":"Songfang Huang","orcid":"https://orcid.org/0000-0001-8084-0904"},"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":"Songfang Huang","raw_affiliation_strings":["Alibaba Damo Academy, Hangzhou, China"],"affiliations":[{"raw_affiliation_string":"Alibaba Damo Academy, Hangzhou, China","institution_ids":["https://openalex.org/I45928872"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030015771","display_name":"Ka\u2010Chun Wong","orcid":"https://orcid.org/0000-0001-6062-733X"},"institutions":[{"id":"https://openalex.org/I168719708","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23","country_code":"HK","type":"education","lineage":["https://openalex.org/I168719708"]},{"id":"https://openalex.org/I4210105229","display_name":"City University of Hong Kong, Shenzhen Research Institute","ror":"https://ror.org/00xc0ma20","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210105229"]}],"countries":["CN","HK"],"is_corresponding":false,"raw_author_name":"Ka-Chun Wong","raw_affiliation_strings":["Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong SAR","Hong Kong Institute for Data Science, City University of Hong Kong, Kowloon, Hong Kong","Shenzhen Research Institute, City University of Hong Kong, Shenzhen, China"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong SAR","institution_ids":["https://openalex.org/I168719708"]},{"raw_affiliation_string":"Hong Kong Institute for Data Science, City University of Hong Kong, Kowloon, Hong Kong","institution_ids":["https://openalex.org/I168719708"]},{"raw_affiliation_string":"Shenzhen Research Institute, City University of Hong Kong, Shenzhen, China","institution_ids":["https://openalex.org/I168719708","https://openalex.org/I4210105229"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5091899643","display_name":"Yaoyun Zhang","orcid":"https://orcid.org/0000-0001-9220-3101"},"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":"Yaoyun Zhang","raw_affiliation_strings":["Alibaba Damo Academy, Hangzhou, China"],"affiliations":[{"raw_affiliation_string":"Alibaba Damo Academy, Hangzhou, China","institution_ids":["https://openalex.org/I45928872"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":12,"corresponding_author_ids":["https://openalex.org/A5100727472"],"corresponding_institution_ids":["https://openalex.org/I168719708"],"apc_list":null,"apc_paid":null,"fwci":1.4468,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.82480659,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":97,"max":98},"biblio":{"volume":"5","issue":"9","first_page":"4595","last_page":"4606"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9997000098228455,"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":0.9997000098228455,"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/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/2741","display_name":"Radiology, Nuclear Medicine and Imaging"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10755","display_name":"HER2/EGFR in Cancer Research","score":0.9986000061035156,"subfield":{"id":"https://openalex.org/subfields/2730","display_name":"Oncology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/dual","display_name":"Dual (grammatical number)","score":0.7016014456748962},{"id":"https://openalex.org/keywords/diffusion","display_name":"Diffusion","score":0.5266901254653931},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.5067840218544006},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4053935706615448},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.2776353359222412},{"id":"https://openalex.org/keywords/quantum-mechanics","display_name":"Quantum mechanics","score":0.08384960889816284}],"concepts":[{"id":"https://openalex.org/C2780980858","wikidata":"https://www.wikidata.org/wiki/Q110022","display_name":"Dual (grammatical number)","level":2,"score":0.7016014456748962},{"id":"https://openalex.org/C69357855","wikidata":"https://www.wikidata.org/wiki/Q163214","display_name":"Diffusion","level":2,"score":0.5266901254653931},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.5067840218544006},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4053935706615448},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.2776353359222412},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.08384960889816284},{"id":"https://openalex.org/C142362112","wikidata":"https://www.wikidata.org/wiki/Q735","display_name":"Art","level":0,"score":0.0},{"id":"https://openalex.org/C124952713","wikidata":"https://www.wikidata.org/wiki/Q8242","display_name":"Literature","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/tai.2024.3387402","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tai.2024.3387402","pdf_url":null,"source":{"id":"https://openalex.org/S4210169448","display_name":"IEEE Transactions on Artificial Intelligence","issn_l":"2691-4581","issn":["2691-4581"],"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 Transactions on Artificial Intelligence","raw_type":"journal-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1164128992","display_name":null,"funder_award_id":"CityU 9667265","funder_id":"https://openalex.org/F4320309893","funder_display_name":"City University of Hong Kong"},{"id":"https://openalex.org/G6278479301","display_name":null,"funder_award_id":"32170654","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8797692665","display_name":null,"funder_award_id":"32000464","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320309893","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23"},{"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":60,"referenced_works":["https://openalex.org/W1544009106","https://openalex.org/W1808513053","https://openalex.org/W1918079945","https://openalex.org/W2038586428","https://openalex.org/W2044025814","https://openalex.org/W2052907531","https://openalex.org/W2064264167","https://openalex.org/W2086286404","https://openalex.org/W2119899377","https://openalex.org/W2153972688","https://openalex.org/W2313297207","https://openalex.org/W2402506318","https://openalex.org/W2529996553","https://openalex.org/W2770335515","https://openalex.org/W2783897572","https://openalex.org/W2806351858","https://openalex.org/W2887447356","https://openalex.org/W2900694120","https://openalex.org/W2918544128","https://openalex.org/W2951428751","https://openalex.org/W2957050889","https://openalex.org/W2994860160","https://openalex.org/W2997397781","https://openalex.org/W2999242200","https://openalex.org/W3005769002","https://openalex.org/W3017013979","https://openalex.org/W3035011799","https://openalex.org/W3036527662","https://openalex.org/W3080588469","https://openalex.org/W3099414221","https://openalex.org/W3112376646","https://openalex.org/W3113177135","https://openalex.org/W3116865743","https://openalex.org/W3194855384","https://openalex.org/W3209056694","https://openalex.org/W3213998394","https://openalex.org/W4205463297","https://openalex.org/W4242372416","https://openalex.org/W4287083626","https://openalex.org/W4295080598","https://openalex.org/W4297951436","https://openalex.org/W4307178567","https://openalex.org/W4320340371","https://openalex.org/W4327550249","https://openalex.org/W4382239902","https://openalex.org/W4393181728","https://openalex.org/W6679045638","https://openalex.org/W6747927160","https://openalex.org/W6763594095","https://openalex.org/W6771848067","https://openalex.org/W6780226713","https://openalex.org/W6787995345","https://openalex.org/W6789743973","https://openalex.org/W6798447524","https://openalex.org/W6802320626","https://openalex.org/W6804214328","https://openalex.org/W6809609761","https://openalex.org/W6810983538","https://openalex.org/W6843464061","https://openalex.org/W6850533701"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052","https://openalex.org/W2382290278","https://openalex.org/W4395014643"],"abstract_inverted_index":{"Advances":[0],"in":[1,107,138],"deep":[2,57],"generative":[3,58],"models":[4,137],"shed":[5],"light":[6],"on":[7,61,86],"de":[8],"novo":[9],"molecule":[10,16,68,186],"generation":[11,17,69,106],"with":[12],"desired":[13],"properties.":[14],"However,":[15],"targeted":[18],"for":[19,34,65,188],"dual":[20,131,174],"protein":[21,29,80,93],"targets":[22,175,193],"still":[23],"faces":[24],"formidable":[25],"challenges":[26],"including":[27],"insufficient":[28,184],"3D":[30],"structure":[31],"data":[32,187],"requisition":[33],"conditioned":[35],"model":[36,43,64,189],"training,":[37],"inflexibility":[38],"of":[39,79,92,140,167,183],"auto-regressive":[40],"sampling,":[41],"and":[42,82,94,97,125,154,176],"generalization":[44],"to":[45,70,103,116,169,172],"unseen":[46,173],"targets.":[47],"Here,":[48],"this":[49],"study":[50],"proposed":[51],"DiffDTM,":[52],"a":[53,62,108],"novel":[54],"unified":[55],"structure-free":[56],"framework":[59],"based":[60,67],"diffusion":[63],"dual-target":[66],"address":[71],"the":[72,134,165,181],"above":[73],"issues.":[74],"Specifically,":[75],"DiffDTM":[76,119,145,168],"receives":[77],"representations":[78],"sequences":[81],"molecular":[83,95],"graphs":[84],"pretrained":[85],"large-scale":[87],"datasets":[88],"as":[89,159],"inputs":[90],"instead":[91],"conformations":[96],"incorporates":[98],"an":[99],"information":[100],"fusion":[101],"module":[102],"achieve":[104],"conditional":[105],"one-shot":[109],"manner.":[110],"We":[111],"perform":[112],"comprehensive":[113],"multi-view":[114],"experiments":[115],"demonstrate":[117],"that":[118],"can":[120],"generate":[121,148,177],"drug-like,":[122],"synthesis-accessible,":[123],"novel,":[124],"high-binding":[126],"affinity":[127],"molecules":[128,149],"targeting":[129],"specific":[130],"proteins,":[132],"outperforming":[133],"state-of-the-art":[135],"(SOTA)":[136],"terms":[139],"multiple":[141],"evaluation":[142],"metrics.":[143],"Furthermore,":[144],"could":[146],"directly":[147],"toward":[150],"dopamine":[151],"receptor":[152,157],"D2":[153],"5-":[155],"hydroxytryptamine":[156],"1A":[158],"new":[160,192],"antipsychotics.":[161],"Experimental":[162],"comparisons":[163],"highlight":[164],"generalizability":[166],"easily":[170],"adapt":[171],"bioactive":[178],"molecules,":[179],"addressing":[180],"issues":[182],"active":[185],"training":[190],"when":[191],"are":[194],"encountered.":[195]},"counts_by_year":[{"year":2025,"cited_by_count":4}],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}