{"id":"https://openalex.org/W7126116012","doi":"https://doi.org/10.1109/bibm66473.2025.11356659","title":"SWEC-DTA: Slide-Window Transformer and ECAttention Method for Predicting Drug-Target Binding Affinity","display_name":"SWEC-DTA: Slide-Window Transformer and ECAttention Method for Predicting Drug-Target Binding Affinity","publication_year":2025,"publication_date":"2025-12-15","ids":{"openalex":"https://openalex.org/W7126116012","doi":"https://doi.org/10.1109/bibm66473.2025.11356659"},"language":null,"primary_location":{"id":"doi:10.1109/bibm66473.2025.11356659","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm66473.2025.11356659","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2025 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-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/A5124168406","display_name":"Yu-Jiang Cheng","orcid":null},"institutions":[{"id":"https://openalex.org/I2722730","display_name":"Inner Mongolia University","ror":"https://ror.org/0106qb496","country_code":"CN","type":"education","lineage":["https://openalex.org/I2722730"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Yu-Jiang Cheng","raw_affiliation_strings":["Inner Mongolia University,Department of Computer Science,Hohhot,China"],"affiliations":[{"raw_affiliation_string":"Inner Mongolia University,Department of Computer Science,Hohhot,China","institution_ids":["https://openalex.org/I2722730"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5124226290","display_name":"Juan Wang","orcid":null},"institutions":[{"id":"https://openalex.org/I2722730","display_name":"Inner Mongolia University","ror":"https://ror.org/0106qb496","country_code":"CN","type":"education","lineage":["https://openalex.org/I2722730"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Juan Wang","raw_affiliation_strings":["Inner Mongolia University,Department of Computer Science,Hohhot,China"],"affiliations":[{"raw_affiliation_string":"Inner Mongolia University,Department of Computer Science,Hohhot,China","institution_ids":["https://openalex.org/I2722730"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5124206099","display_name":"Shang-Jun Yang","orcid":null},"institutions":[{"id":"https://openalex.org/I2722730","display_name":"Inner Mongolia University","ror":"https://ror.org/0106qb496","country_code":"CN","type":"education","lineage":["https://openalex.org/I2722730"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shang-Jun Yang","raw_affiliation_strings":["Inner Mongolia University,Department of Computer Science,Hohhot,China"],"affiliations":[{"raw_affiliation_string":"Inner Mongolia University,Department of Computer Science,Hohhot,China","institution_ids":["https://openalex.org/I2722730"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5124150511","display_name":"Yuan Zhang","orcid":null},"institutions":[{"id":"https://openalex.org/I2722730","display_name":"Inner Mongolia University","ror":"https://ror.org/0106qb496","country_code":"CN","type":"education","lineage":["https://openalex.org/I2722730"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yuan Zhang","raw_affiliation_strings":["Inner Mongolia University,Department of Computer Science,Hohhot,China"],"affiliations":[{"raw_affiliation_string":"Inner Mongolia University,Department of Computer Science,Hohhot,China","institution_ids":["https://openalex.org/I2722730"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5124246382","display_name":"Xiang-Zhen Song","orcid":null},"institutions":[{"id":"https://openalex.org/I2722730","display_name":"Inner Mongolia University","ror":"https://ror.org/0106qb496","country_code":"CN","type":"education","lineage":["https://openalex.org/I2722730"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiang-Zhen Song","raw_affiliation_strings":["Inner Mongolia University,Department of Computer Science,Hohhot,China"],"affiliations":[{"raw_affiliation_string":"Inner Mongolia University,Department of Computer Science,Hohhot,China","institution_ids":["https://openalex.org/I2722730"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5124168406"],"corresponding_institution_ids":["https://openalex.org/I2722730"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.75670361,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"765","last_page":"768"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.8629999756813049,"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":0.8629999756813049,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.05559999868273735,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.04410000145435333,"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/sliding-window-protocol","display_name":"Sliding window protocol","score":0.6335999965667725},{"id":"https://openalex.org/keywords/transformer","display_name":"Transformer","score":0.5526999831199646},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4821999967098236},{"id":"https://openalex.org/keywords/protein-sequencing","display_name":"Protein sequencing","score":0.3950999975204468},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.35499998927116394},{"id":"https://openalex.org/keywords/channel","display_name":"Channel (broadcasting)","score":0.34700000286102295}],"concepts":[{"id":"https://openalex.org/C102392041","wikidata":"https://www.wikidata.org/wiki/Q592860","display_name":"Sliding window protocol","level":3,"score":0.6335999965667725},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6101999878883362},{"id":"https://openalex.org/C66322947","wikidata":"https://www.wikidata.org/wiki/Q11658","display_name":"Transformer","level":3,"score":0.5526999831199646},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4821999967098236},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.43970000743865967},{"id":"https://openalex.org/C10010492","wikidata":"https://www.wikidata.org/wiki/Q3142557","display_name":"Protein sequencing","level":4,"score":0.3950999975204468},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3896999955177307},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.35499998927116394},{"id":"https://openalex.org/C127162648","wikidata":"https://www.wikidata.org/wiki/Q16858953","display_name":"Channel (broadcasting)","level":2,"score":0.34700000286102295},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.3418000042438507},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.3303999900817871},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3278999924659729},{"id":"https://openalex.org/C112972136","wikidata":"https://www.wikidata.org/wiki/Q7595718","display_name":"Stability (learning theory)","level":2,"score":0.32089999318122864},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3109000027179718},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3070000112056732},{"id":"https://openalex.org/C2989108626","wikidata":"https://www.wikidata.org/wiki/Q904407","display_name":"Drug target","level":2,"score":0.29280000925064087},{"id":"https://openalex.org/C46622094","wikidata":"https://www.wikidata.org/wiki/Q659446","display_name":"Therapeutic window","level":2,"score":0.28540000319480896},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.2849000096321106},{"id":"https://openalex.org/C2778751112","wikidata":"https://www.wikidata.org/wiki/Q835016","display_name":"Window (computing)","level":2,"score":0.25099998712539673}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm66473.2025.11356659","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm66473.2025.11356659","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2025 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G8345816191","display_name":null,"funder_award_id":"2025YFHH0053","funder_id":"https://openalex.org/F4320328958","funder_display_name":"Department of Science and Technology of Inner Mongolia"}],"funders":[{"id":"https://openalex.org/F4320328958","display_name":"Department of Science and Technology of Inner Mongolia","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":5,"referenced_works":["https://openalex.org/W4205167309","https://openalex.org/W4390140606","https://openalex.org/W4390883205","https://openalex.org/W4406261360","https://openalex.org/W4407117450"],"related_works":[],"abstract_inverted_index":{"Precise":[0],"drug-target":[1],"affinity":[2],"(DTA)":[3],"prediction":[4,14],"is":[5,78,116,127],"essential":[6],"for":[7,85],"accelerating":[8],"drug":[9,63],"discovery":[10],"pipeline.":[11],"To":[12],"improve":[13],"accuracy,":[15],"in":[16],"this":[17],"paper,":[18],"we":[19,157],"utilized":[20],"two":[21],"new":[22,41],"datasets":[23],"based":[24,46],"on":[25,143,164],"the":[26,58,62,65,70,87,90,94,112,132,168,171],"BindingDB":[27],"database,":[28],"which":[29,45],"have":[30],"been":[31,139],"updated":[32],"with":[33],"newly":[34],"discovered":[35],"DTA":[36],"data.":[37],"We":[38],"propose":[39],"a":[40,99],"method":[42],"called":[43],"SWEC-DTA,":[44],"sliding":[47],"window":[48,75],"attention":[49,54],"mechanism":[50],"and":[51,64,89,102,122,141,161],"efficient":[52],"channel":[53],"mechanism.":[55],"It":[56],"takes":[57],"SMILES":[59,96],"sequence":[60,68,83,97],"of":[61,69,170],"amino":[66],"acid":[67],"protein":[71,88,120],"as":[72],"input.":[73],"Sliding":[74],"transformer":[76],"(SWIN)":[77],"used":[79,128],"to":[80,110,118,129,166],"obtain":[81,119],"1D":[82],"features":[84],"both":[86],"drug.":[91],"After":[92],"converting":[93],"drug's":[95],"into":[98],"molecular":[100,103],"graph":[101],"fingerprints":[104],"(MACCS,":[105],"PubChem,":[106],"ErG)":[107],"are":[108],"combined":[109],"enhance":[111],"2D":[113],"representation.":[114],"ESM":[115],"employed":[117],"evolutionary":[121],"functional":[123],"features.":[124,136],"Finally,":[125],"ECAttention":[126],"dynamically":[130],"learn":[131],"interaction":[133],"relationships":[134],"between":[135],"SWEC-DTA":[137,150],"has":[138],"trained":[140],"tested":[142],"three":[144],"datasets.":[145],"Experimental":[146],"results":[147],"demonstrate":[148],"that":[149],"significantly":[151],"outperforms":[152],"other":[153],"baseline":[154],"methods.":[155],"Additionally,":[156],"conducted":[158],"ablation":[159],"experiments":[160],"parameter":[162],"optimization":[163],"DB_KD":[165],"validate":[167],"effectiveness":[169],"method.":[172]},"counts_by_year":[],"updated_date":"2026-04-09T08:11:56.329763","created_date":"2026-01-30T00:00:00"}
