{"id":"https://openalex.org/W4409228374","doi":"https://doi.org/10.1109/tcbbio.2025.3558695","title":"SSRAAI: Learning Sequence and Structural Representations to Predict Antibody-Antigen Interactions","display_name":"SSRAAI: Learning Sequence and Structural Representations to Predict Antibody-Antigen Interactions","publication_year":2025,"publication_date":"2025-04-07","ids":{"openalex":"https://openalex.org/W4409228374","doi":"https://doi.org/10.1109/tcbbio.2025.3558695","pmid":"https://pubmed.ncbi.nlm.nih.gov/40811345"},"language":"en","primary_location":{"id":"doi:10.1109/tcbbio.2025.3558695","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2025.3558695","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":"Bin Wang","orcid":"https://orcid.org/0000-0001-7771-5360"},"institutions":[{"id":"https://openalex.org/I9086337","display_name":"Taiyuan University of Technology","ror":"https://ror.org/03kv08d37","country_code":"CN","type":"education","lineage":["https://openalex.org/I9086337"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Bin Wang","raw_affiliation_strings":["School of Computer Science and Technology (School of Data Science), Taiyuan University of Technology, Taiyuan, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology (School of Data Science), Taiyuan University of Technology, Taiyuan, China","institution_ids":["https://openalex.org/I9086337"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Hongye Yang","orcid":"https://orcid.org/0009-0005-6238-2555"},"institutions":[{"id":"https://openalex.org/I9086337","display_name":"Taiyuan University of Technology","ror":"https://ror.org/03kv08d37","country_code":"CN","type":"education","lineage":["https://openalex.org/I9086337"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hongye Yang","raw_affiliation_strings":["School of Computer Science and Technology (School of Data Science), Taiyuan University of Technology, Taiyuan, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology (School of Data Science), Taiyuan University of Technology, Taiyuan, China","institution_ids":["https://openalex.org/I9086337"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Jiarui Liang","orcid":"https://orcid.org/0000-0001-9827-8104"},"institutions":[{"id":"https://openalex.org/I9086337","display_name":"Taiyuan University of Technology","ror":"https://ror.org/03kv08d37","country_code":"CN","type":"education","lineage":["https://openalex.org/I9086337"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jiarui Liang","raw_affiliation_strings":["School of Computer Science and Technology (School of Data Science), Taiyuan University of Technology, Taiyuan, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology (School of Data Science), Taiyuan University of Technology, Taiyuan, China","institution_ids":["https://openalex.org/I9086337"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014284755","display_name":"Songhui Rao","orcid":"https://orcid.org/0009-0002-8067-4496"},"institutions":[{"id":"https://openalex.org/I9086337","display_name":"Taiyuan University of Technology","ror":"https://ror.org/03kv08d37","country_code":"CN","type":"education","lineage":["https://openalex.org/I9086337"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Songhui Rao","raw_affiliation_strings":["School of Computer Science and Technology (School of Data Science), Taiyuan University of Technology, Taiyuan, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology (School of Data Science), Taiyuan University of Technology, Taiyuan, China","institution_ids":["https://openalex.org/I9086337"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5109441481","display_name":"Ting Yan","orcid":null},"institutions":[{"id":"https://openalex.org/I17721919","display_name":"Shanxi Medical University","ror":"https://ror.org/0265d1010","country_code":"CN","type":"education","lineage":["https://openalex.org/I17721919"]},{"id":"https://openalex.org/I4210133678","display_name":"Second Hospital of Shanxi Medical University","ror":"https://ror.org/03tn5kh37","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210133678"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ting Yan","raw_affiliation_strings":["Shanxi Key Laboratory of Bone and Soft Tissue Injury Repair, Shanxi Medical University, Taiyuan, China","Translational Medicine Research Center, Shanxi Medical University, Taiyuan, China"],"affiliations":[{"raw_affiliation_string":"Shanxi Key Laboratory of Bone and Soft Tissue Injury Repair, Shanxi Medical University, Taiyuan, China","institution_ids":["https://openalex.org/I17721919","https://openalex.org/I4210133678"]},{"raw_affiliation_string":"Translational Medicine Research Center, Shanxi Medical University, Taiyuan, China","institution_ids":["https://openalex.org/I17721919"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5115595638","display_name":"Yu-Hui Liu","orcid":"https://orcid.org/0009-0004-7700-3522"},"institutions":[{"id":"https://openalex.org/I9086337","display_name":"Taiyuan University of Technology","ror":"https://ror.org/03kv08d37","country_code":"CN","type":"education","lineage":["https://openalex.org/I9086337"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yuhui Liu","raw_affiliation_strings":["School of Computer Science and Technology (School of Data Science), Taiyuan University of Technology, Taiyuan, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology (School of Data Science), Taiyuan University of Technology, Taiyuan, China","institution_ids":["https://openalex.org/I9086337"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056771708","display_name":"Xinyun Li","orcid":"https://orcid.org/0000-0002-7943-1713"},"institutions":[{"id":"https://openalex.org/I9086337","display_name":"Taiyuan University of Technology","ror":"https://ror.org/03kv08d37","country_code":"CN","type":"education","lineage":["https://openalex.org/I9086337"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xinyun Li","raw_affiliation_strings":["School of Computer Science and Technology (School of Data Science), Taiyuan University of Technology, Taiyuan, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology (School of Data Science), Taiyuan University of Technology, Taiyuan, China","institution_ids":["https://openalex.org/I9086337"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Jie Xiang","orcid":"https://orcid.org/0000-0002-9758-6954"},"institutions":[{"id":"https://openalex.org/I9086337","display_name":"Taiyuan University of Technology","ror":"https://ror.org/03kv08d37","country_code":"CN","type":"education","lineage":["https://openalex.org/I9086337"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jie Xiang","raw_affiliation_strings":["School of Computer Science and Technology (School of Data Science), Taiyuan University of Technology, Taiyuan, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology (School of Data Science), Taiyuan University of Technology, Taiyuan, China","institution_ids":["https://openalex.org/I9086337"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101815036","display_name":"Huiqing Wang","orcid":"https://orcid.org/0000-0001-8611-6546"},"institutions":[{"id":"https://openalex.org/I9086337","display_name":"Taiyuan University of Technology","ror":"https://ror.org/03kv08d37","country_code":"CN","type":"education","lineage":["https://openalex.org/I9086337"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Huiqing Wang","raw_affiliation_strings":["School of Computer Science and Technology (School of Data Science), Taiyuan University of Technology, Taiyuan, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology (School of Data Science), Taiyuan University of Technology, Taiyuan, China","institution_ids":["https://openalex.org/I9086337"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Yu Xia","orcid":"https://orcid.org/0000-0002-5596-5518"},"institutions":[{"id":"https://openalex.org/I5023651","display_name":"McGill University","ror":"https://ror.org/01pxwe438","country_code":"CA","type":"education","lineage":["https://openalex.org/I5023651"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Yu Xia","raw_affiliation_strings":["Department of Bioengineering, McGill University, Montreal, QC, Canada","Department of Bioengineering, McGill Uni-versity, Montreal, Quebec, Canada"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, McGill University, Montreal, QC, Canada","institution_ids":["https://openalex.org/I5023651"]},{"raw_affiliation_string":"Department of Bioengineering, McGill Uni-versity, Montreal, Quebec, Canada","institution_ids":["https://openalex.org/I5023651"]}]},{"author_position":"last","author":{"id":null,"display_name":"Ying Li","orcid":"https://orcid.org/0009-0009-5236-6745"},"institutions":[{"id":"https://openalex.org/I9086337","display_name":"Taiyuan University of Technology","ror":"https://ror.org/03kv08d37","country_code":"CN","type":"education","lineage":["https://openalex.org/I9086337"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ying Li","raw_affiliation_strings":["School of Computer Science and Technology (School of Data Science), Taiyuan University of Technology, Taiyuan, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology (School of Data Science), Taiyuan University of Technology, Taiyuan, China","institution_ids":["https://openalex.org/I9086337"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":11,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I9086337"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.10451316,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"22","issue":"4","first_page":"1467","last_page":"1478"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":0.9991000294685364,"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"}},"topics":[{"id":"https://openalex.org/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":0.9991000294685364,"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/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.9818999767303467,"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/T10602","display_name":"Glycosylation and Glycoproteins Research","score":0.9714000225067139,"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/sequence","display_name":"Sequence (biology)","score":0.6012591123580933},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5384070873260498},{"id":"https://openalex.org/keywords/antigen","display_name":"Antigen","score":0.4945776164531708},{"id":"https://openalex.org/keywords/antibody","display_name":"Antibody","score":0.471492737531662},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.44896838068962097},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.30676186084747314},{"id":"https://openalex.org/keywords/immunology","display_name":"Immunology","score":0.25070565938949585},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1692236065864563}],"concepts":[{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.6012591123580933},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5384070873260498},{"id":"https://openalex.org/C147483822","wikidata":"https://www.wikidata.org/wiki/Q103537","display_name":"Antigen","level":2,"score":0.4945776164531708},{"id":"https://openalex.org/C159654299","wikidata":"https://www.wikidata.org/wiki/Q79460","display_name":"Antibody","level":2,"score":0.471492737531662},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.44896838068962097},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.30676186084747314},{"id":"https://openalex.org/C203014093","wikidata":"https://www.wikidata.org/wiki/Q101929","display_name":"Immunology","level":1,"score":0.25070565938949585},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1692236065864563}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbbio.2025.3558695","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2025.3558695","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:40811345","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40811345","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":[{"id":"https://openalex.org/G4207980392","display_name":null,"funder_award_id":"CSC 202406930001","funder_id":"https://openalex.org/F4320322725","funder_display_name":"China Scholarship Council"},{"id":"https://openalex.org/G8163008353","display_name":null,"funder_award_id":"62176177","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G881508420","display_name":null,"funder_award_id":"62403344","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"},{"id":"https://openalex.org/F4320322725","display_name":"China Scholarship Council","ror":"https://ror.org/04atp4p48"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":53,"referenced_works":["https://openalex.org/W38209402","https://openalex.org/W1568693476","https://openalex.org/W1979552897","https://openalex.org/W1982607933","https://openalex.org/W1984871500","https://openalex.org/W1985218089","https://openalex.org/W1995129977","https://openalex.org/W2039473152","https://openalex.org/W2066706759","https://openalex.org/W2111973517","https://openalex.org/W2132580736","https://openalex.org/W2150884352","https://openalex.org/W2169760021","https://openalex.org/W2170960297","https://openalex.org/W2559258718","https://openalex.org/W2612935389","https://openalex.org/W2801965704","https://openalex.org/W2808491442","https://openalex.org/W2916691697","https://openalex.org/W2950354111","https://openalex.org/W2957436444","https://openalex.org/W3016492430","https://openalex.org/W3035163373","https://openalex.org/W3037822883","https://openalex.org/W3039131048","https://openalex.org/W3042293051","https://openalex.org/W3048406079","https://openalex.org/W3049166744","https://openalex.org/W3112760082","https://openalex.org/W3133540795","https://openalex.org/W3135883064","https://openalex.org/W3146135000","https://openalex.org/W3156522942","https://openalex.org/W3164228670","https://openalex.org/W3174714560","https://openalex.org/W3177500196","https://openalex.org/W3186179742","https://openalex.org/W3197596721","https://openalex.org/W3215079983","https://openalex.org/W4210520848","https://openalex.org/W4210822321","https://openalex.org/W4210997669","https://openalex.org/W4211015210","https://openalex.org/W4226108318","https://openalex.org/W4255957063","https://openalex.org/W4285414302","https://openalex.org/W4308432368","https://openalex.org/W4312187703","https://openalex.org/W4317703013","https://openalex.org/W4321851522","https://openalex.org/W4362664122","https://openalex.org/W4385245566","https://openalex.org/W4396721167"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2082860237","https://openalex.org/W2119695867","https://openalex.org/W2130076355","https://openalex.org/W1990804418","https://openalex.org/W1993764875","https://openalex.org/W2046158694","https://openalex.org/W2788277189","https://openalex.org/W2013243191","https://openalex.org/W1971568933"],"abstract_inverted_index":{"The":[0],"specific":[1],"binding":[2],"between":[3],"antibodies":[4],"(Ab)":[5],"and":[6,14,48,132,188,196],"antigens":[7],"(Ag)":[8],"is":[9,27],"crucial":[10,28],"for":[11,29],"developing":[12],"drugs":[13],"vaccines":[15],"to":[16,55,95,135,165,186],"treat":[17],"major":[18],"diseases.":[19],"Therefore,":[20],"accurate":[21],"identification":[22],"of":[23,33,60,85,156,175,201],"antibody-antigen":[24,88,137],"interactions":[25,89,138],"(AAI)":[26],"a":[30,172],"comprehensive":[31],"understanding":[32],"antibody":[34],"therapeutic":[35],"mechanisms.":[36],"While":[37],"wet-lab":[38],"methods":[39,53],"accurately":[40],"characterize":[41],"AAI,":[42],"they":[43,71,100],"require":[44],"significant":[45],"human,":[46],"financial,":[47],"time":[49],"costs.":[50],"Traditional":[51],"computational":[52],"help":[54],"reduce":[56],"the":[57,83,107,154,199],"resource":[58],"consumption":[59],"AAI":[61],"identification,":[62],"but":[63],"suffer":[64],"from":[65,148,179],"several":[66],"problems,":[67],"such":[68],"as":[69],"(1)":[70],"rely":[72],"solely":[73],"on":[74,87,103,160,192],"sequence":[75,131,157,182],"data,":[76,183],"ignoring":[77],"critical":[78],"3D":[79,151,176],"structural":[80,133,142,177],"determinants;":[81],"(2)":[82],"scarcity":[84],"data":[86],"severely":[90],"limits":[91],"existing":[92],"methods'":[93],"ability":[94],"represent":[96],"unseen":[97],"antibodies;":[98],"(3)":[99],"focus":[101],"narrowly":[102],"paratope-epitope":[104],"residues,":[105],"overlooking":[106],"contextual":[108],"information":[109,178],"provided":[110],"by":[111,144],"distal":[112],"non-binding":[113],"regions":[114],"that":[115,129],"can":[116],"influence":[117],"interaction":[118],"patterns.":[119],"To":[120],"address":[121],"these":[122],"issues,":[123],"we":[124],"present":[125],"an":[126],"innovative":[127],"model":[128],"learns":[130],"representations":[134],"predict":[136],"(SSRAAI).":[139],"We":[140],"extracted":[141],"features":[143,158],"constructing":[145],"contact":[146],"maps":[147],"predicted":[149],"PDB":[150,180],"structures.":[152],"Additionally,":[153],"integration":[155,174],"based":[159],"adaptive":[161],"relational":[162],"graphs":[163],"led":[164],"enhanced":[166],"prediction":[167],"outcomes.":[168],"Our":[169],"approach":[170,203],"offers":[171],"unique":[173],"with":[181],"applied":[184],"directly":[185],"Ab":[187],"Ag.":[189],"Comparative":[190],"results":[191],"two":[193],"datasets,":[194],"HIV":[195],"SARS-CoV-2,":[197],"demonstrate":[198],"validity":[200],"our":[202],"in":[204],"identifying":[205],"AAIs.":[206]},"counts_by_year":[],"updated_date":"2026-04-09T08:11:56.329763","created_date":"2025-10-10T00:00:00"}
