{"id":"https://openalex.org/W4409641483","doi":"https://doi.org/10.1109/tcbbio.2025.3562876","title":"Multiscale Motif-Aware Relation Graph Structure for Drug-Target Binding Affinity Prediction","display_name":"Multiscale Motif-Aware Relation Graph Structure for Drug-Target Binding Affinity Prediction","publication_year":2025,"publication_date":"2025-04-21","ids":{"openalex":"https://openalex.org/W4409641483","doi":"https://doi.org/10.1109/tcbbio.2025.3562876","pmid":"https://pubmed.ncbi.nlm.nih.gov/40811346"},"language":"en","primary_location":{"id":"doi:10.1109/tcbbio.2025.3562876","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2025.3562876","pdf_url":null,"source":{"id":"https://openalex.org/S5407042751","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"2998-4165","issn":["2998-4165"],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE 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":null,"display_name":"Cheng Cheng","orcid":"https://orcid.org/0009-0002-5316-5768"},"institutions":[{"id":"https://openalex.org/I158842170","display_name":"Chongqing University","ror":"https://ror.org/023rhb549","country_code":"CN","type":"education","lineage":["https://openalex.org/I158842170"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Cheng Cheng","raw_affiliation_strings":["Key Laboratory of Dependable Service Computing in Cyber Physical Society, Ministry of Education, Chongqing University, Chongqing, China","Key Laboratory of Dependable Service Computing in Cyber Physical Society (Chongqing University), Ministry of Education, Chongqing, China"],"raw_orcid":"https://orcid.org/0009-0002-5316-5768","affiliations":[{"raw_affiliation_string":"Key Laboratory of Dependable Service Computing in Cyber Physical Society, Ministry of Education, Chongqing University, Chongqing, China","institution_ids":["https://openalex.org/I158842170"]},{"raw_affiliation_string":"Key Laboratory of Dependable Service Computing in Cyber Physical Society (Chongqing University), Ministry of Education, Chongqing, China","institution_ids":["https://openalex.org/I158842170"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100330109","display_name":"Xiaohong Zhang","orcid":"https://orcid.org/0000-0002-1767-9342"},"institutions":[{"id":"https://openalex.org/I158842170","display_name":"Chongqing University","ror":"https://ror.org/023rhb549","country_code":"CN","type":"education","lineage":["https://openalex.org/I158842170"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaohong Zhang","raw_affiliation_strings":["Key Laboratory of Dependable Service Computing in Cyber Physical Society, Ministry of Education, Chongqing University, Chongqing, China","Key Laboratory of Dependable Service Computing in Cyber Physical Society (Chongqing University), Ministry of Education, Chongqing, China"],"raw_orcid":"https://orcid.org/0000-0002-1767-9342","affiliations":[{"raw_affiliation_string":"Key Laboratory of Dependable Service Computing in Cyber Physical Society, Ministry of Education, Chongqing University, Chongqing, China","institution_ids":["https://openalex.org/I158842170"]},{"raw_affiliation_string":"Key Laboratory of Dependable Service Computing in Cyber Physical Society (Chongqing University), Ministry of Education, Chongqing, China","institution_ids":["https://openalex.org/I158842170"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003048967","display_name":"Mianyang Yu","orcid":"https://orcid.org/0009-0001-8722-2444"},"institutions":[{"id":"https://openalex.org/I158842170","display_name":"Chongqing University","ror":"https://ror.org/023rhb549","country_code":"CN","type":"education","lineage":["https://openalex.org/I158842170"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Mianyang Yu","raw_affiliation_strings":["Key Laboratory of Dependable Service Computing in Cyber Physical Society, Ministry of Education, Chongqing University, Chongqing, China","Key Laboratory of Dependable Service Computing in Cyber Physical Society (Chongqing University), Ministry of Education, Chongqing, China"],"raw_orcid":"https://orcid.org/0009-0001-8722-2444","affiliations":[{"raw_affiliation_string":"Key Laboratory of Dependable Service Computing in Cyber Physical Society, Ministry of Education, Chongqing University, Chongqing, China","institution_ids":["https://openalex.org/I158842170"]},{"raw_affiliation_string":"Key Laboratory of Dependable Service Computing in Cyber Physical Society (Chongqing University), Ministry of Education, Chongqing, China","institution_ids":["https://openalex.org/I158842170"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Yuqin Xia","orcid":"https://orcid.org/0009-0007-3903-0775"},"institutions":[{"id":"https://openalex.org/I158842170","display_name":"Chongqing University","ror":"https://ror.org/023rhb549","country_code":"CN","type":"education","lineage":["https://openalex.org/I158842170"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yuqin Xia","raw_affiliation_strings":["Key Laboratory of Dependable Service Computing in Cyber Physical Society, Ministry of Education, Chongqing University, Chongqing, China","Key Laboratory of Dependable Service Computing in Cyber Physical Society (Chongqing University), Ministry of Education, Chongqing, China"],"raw_orcid":"https://orcid.org/0009-0007-3903-0775","affiliations":[{"raw_affiliation_string":"Key Laboratory of Dependable Service Computing in Cyber Physical Society, Ministry of Education, Chongqing University, Chongqing, China","institution_ids":["https://openalex.org/I158842170"]},{"raw_affiliation_string":"Key Laboratory of Dependable Service Computing in Cyber Physical Society (Chongqing University), Ministry of Education, Chongqing, China","institution_ids":["https://openalex.org/I158842170"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5027345342","display_name":"Weiwei Xue","orcid":"https://orcid.org/0000-0002-3285-0574"},"institutions":[{"id":"https://openalex.org/I158842170","display_name":"Chongqing University","ror":"https://ror.org/023rhb549","country_code":"CN","type":"education","lineage":["https://openalex.org/I158842170"]},{"id":"https://openalex.org/I4210165444","display_name":"Chongqing Medical and Pharmaceutical College","ror":"https://ror.org/05gvw2741","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210165444"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Weiwei Xue","raw_affiliation_strings":["Pharmaceutical Sciences, Chongqing University, Chongqing, China"],"raw_orcid":"https://orcid.org/0000-0002-3285-0574","affiliations":[{"raw_affiliation_string":"Pharmaceutical Sciences, Chongqing University, Chongqing, China","institution_ids":["https://openalex.org/I4210165444","https://openalex.org/I158842170"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.0833291,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"22","issue":"4","first_page":"1615","last_page":"1628"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9994000196456909,"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":0.9994000196456909,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9614999890327454,"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/T10911","display_name":"Chemical Synthesis and Analysis","score":0.9485999941825867,"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/motif","display_name":"Motif (music)","score":0.6207877397537231},{"id":"https://openalex.org/keywords/drug","display_name":"Drug","score":0.4920305907726288},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.48790404200553894},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4853774309158325},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.41020727157592773},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.35399746894836426},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.20317775011062622},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.20183905959129333},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.19328844547271729},{"id":"https://openalex.org/keywords/pharmacology","display_name":"Pharmacology","score":0.19052952527999878},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.11913895606994629}],"concepts":[{"id":"https://openalex.org/C32276052","wikidata":"https://www.wikidata.org/wiki/Q908349","display_name":"Motif (music)","level":2,"score":0.6207877397537231},{"id":"https://openalex.org/C2780035454","wikidata":"https://www.wikidata.org/wiki/Q8386","display_name":"Drug","level":2,"score":0.4920305907726288},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.48790404200553894},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4853774309158325},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.41020727157592773},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.35399746894836426},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.20317775011062622},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.20183905959129333},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.19328844547271729},{"id":"https://openalex.org/C98274493","wikidata":"https://www.wikidata.org/wiki/Q128406","display_name":"Pharmacology","level":1,"score":0.19052952527999878},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.11913895606994629},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbbio.2025.3562876","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2025.3562876","pdf_url":null,"source":{"id":"https://openalex.org/S5407042751","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"2998-4165","issn":["2998-4165"],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40811346","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40811346","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 transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":45,"referenced_works":["https://openalex.org/W1521626043","https://openalex.org/W1975147762","https://openalex.org/W1985270532","https://openalex.org/W1989129581","https://openalex.org/W1992787746","https://openalex.org/W2015292449","https://openalex.org/W2035585923","https://openalex.org/W2062941476","https://openalex.org/W2065854198","https://openalex.org/W2086286404","https://openalex.org/W2109991441","https://openalex.org/W2293078015","https://openalex.org/W2318794083","https://openalex.org/W2592742128","https://openalex.org/W2785947426","https://openalex.org/W2809216727","https://openalex.org/W2883535080","https://openalex.org/W2951433247","https://openalex.org/W2990045899","https://openalex.org/W3032123378","https://openalex.org/W3034971973","https://openalex.org/W3096561213","https://openalex.org/W3107681958","https://openalex.org/W3177828909","https://openalex.org/W3207312583","https://openalex.org/W4205167309","https://openalex.org/W4243568023","https://openalex.org/W4308055347","https://openalex.org/W4309452766","https://openalex.org/W4317931697","https://openalex.org/W4318624508","https://openalex.org/W4322745247","https://openalex.org/W4375863032","https://openalex.org/W4385330534","https://openalex.org/W4386702974","https://openalex.org/W4386898749","https://openalex.org/W4389317742","https://openalex.org/W4392239460","https://openalex.org/W4401730694","https://openalex.org/W6631190155","https://openalex.org/W6640963894","https://openalex.org/W6679436768","https://openalex.org/W6726873649","https://openalex.org/W6784526300","https://openalex.org/W6859070344"],"related_works":["https://openalex.org/W4387497383","https://openalex.org/W2948807893","https://openalex.org/W2899084033","https://openalex.org/W2778153218","https://openalex.org/W2748952813","https://openalex.org/W1531601525","https://openalex.org/W4391375266","https://openalex.org/W2078814861","https://openalex.org/W2527526854","https://openalex.org/W1976181487"],"abstract_inverted_index":{"Exploring":[0],"drug-target":[1,22,142,163,185],"binding":[2],"affinity":[3,43,164,186],"(DTA)":[4],"is":[5,36],"essential":[6],"for":[7,20,93,100,116],"drug":[8,31,63],"discovery.":[9],"Numerous":[10],"works":[11],"rely":[12],"on":[13,147],"the":[14,26,42,50,58,78,134,148,178,184,195],"one-dimensional":[15],"SMILES":[16,59],"representation":[17,60],"of":[18,30,45,74,81,170,180],"drugs":[19],"predicting":[21],"affinity,":[23],"but":[24],"ignore":[25],"crucial":[27,68],"structural":[28,34,70,103],"information":[29,35,73,104,119],"molecules.":[32],"Considering":[33],"an":[37,167],"important":[38],"factor":[39],"in":[40,162],"determining":[41],"properties":[44],"drugs,":[46,75,94],"we":[47,86],"propose":[48,87],"using":[49],"multiscale":[51,97],"motif-aware":[52,98],"relation":[53,112],"graph":[54,113,126],"(MMRG)":[55],"rather":[56],"than":[57],"to":[61,129,140,182],"build":[62],"descriptors.":[64],"MMRG":[65,90,181],"explicitly":[66],"provides":[67],"motif-level":[69,102],"and":[71,110,133,150,172],"topological":[72,118],"thereby":[76],"ameliorating":[77],"predictive":[79],"power":[80],"models.":[82],"With":[83],"this":[84],"idea,":[85],"a":[88,96,111,125],"novel":[89],"construction":[91,114],"approach":[92,115],"including":[95],"learning":[99],"extracting":[101,117],"from":[105,120,131],"motifs":[106],"with":[107,166,194],"different":[108],"sizes":[109],"chemical":[121],"bonds.":[122],"We":[123,175],"implement":[124],"convolutional":[127],"network":[128],"learn":[130],"MMRGs,":[132],"learned":[135],"latent":[136],"features":[137],"are":[138],"used":[139],"predict":[141],"affinity.":[143],"The":[144],"experiment":[145],"results":[146],"Davis":[149],"KIBA":[151],"dataset":[152],"report":[153],"that":[154],"our":[155],"model":[156],"can":[157],"significantly":[158],"outperform":[159],"existing":[160],"methods":[161],"prediction,":[165],"average":[168],"improvement":[169],"15.61%":[171],"8.50%":[173],"respectively.":[174],"further":[176],"explain":[177],"principle":[179],"improve":[183],"prediction":[187],"accuracy":[188],"by":[189],"comparing":[190],"its":[191],"generative":[192],"function":[193],"state-of-the-art":[196],"method.":[197]},"counts_by_year":[],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
