{"id":"https://openalex.org/W7137056126","doi":"https://doi.org/10.1093/bib/bbag048","title":"Decoding TCR recognition via geometric deep learning of immunological fingerprints","display_name":"Decoding TCR recognition via geometric deep learning of immunological fingerprints","publication_year":2026,"publication_date":"2026-03-01","ids":{"openalex":"https://openalex.org/W7137056126","doi":"https://doi.org/10.1093/bib/bbag048","pmid":"https://pubmed.ncbi.nlm.nih.gov/41834397"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbag048","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbag048","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in 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/10.1093/bib/bbag048","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5059112910","display_name":"Chun Min Shang","orcid":null},"institutions":[{"id":"https://openalex.org/I4210137766","display_name":"Institute for Advanced Study","ror":"https://ror.org/03xg85719","country_code":"DE","type":"facility","lineage":["https://openalex.org/I4210137766"]},{"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","DE"],"is_corresponding":true,"raw_author_name":"Chun Shang","raw_affiliation_strings":["College of Physics, College of Life Sciences, and Institute of Quantitative Biology, Zhejiang University , 866 Yuhangtang Road, Hangzhou 310058,","Shanghai Institute for Advanced Study, Zhejiang University , 799 Dangui Road, Shanghai 201203,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Physics, College of Life Sciences, and Institute of Quantitative Biology, Zhejiang University , 866 Yuhangtang Road, Hangzhou 310058,","institution_ids":["https://openalex.org/I76130692"]},{"raw_affiliation_string":"Shanghai Institute for Advanced Study, Zhejiang University , 799 Dangui Road, Shanghai 201203,","institution_ids":["https://openalex.org/I4210137766"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091519403","display_name":"Chun Chan","orcid":"https://orcid.org/0000-0002-3705-1835"},"institutions":[{"id":"https://openalex.org/I69356397","display_name":"Xi\u2019an Jiaotong-Liverpool University","ror":"https://ror.org/03zmrmn05","country_code":"CN","type":"education","lineage":["https://openalex.org/I69356397"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Kevin C Chan","raw_affiliation_strings":["Department of Biosciences and Bioinformatics, School of Science, Xi\u2019an Jiaotong\u2013Liverpool University , 111 Ren\u2019ai Road, Suzhou 215123,"],"raw_orcid":"https://orcid.org/0000-0002-3705-1835","affiliations":[{"raw_affiliation_string":"Department of Biosciences and Bioinformatics, School of Science, Xi\u2019an Jiaotong\u2013Liverpool University , 111 Ren\u2019ai Road, Suzhou 215123,","institution_ids":["https://openalex.org/I69356397"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5078014032","display_name":"Ruhong Zhou","orcid":"https://orcid.org/0000-0001-8624-5591"},"institutions":[{"id":"https://openalex.org/I4210094450","display_name":"First People's Hospital of Yuhang District","ror":"https://ror.org/00nt56514","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210094450"]},{"id":"https://openalex.org/I4210137766","display_name":"Institute for Advanced Study","ror":"https://ror.org/03xg85719","country_code":"DE","type":"facility","lineage":["https://openalex.org/I4210137766"]},{"id":"https://openalex.org/I4210166576","display_name":"First Affiliated Hospital Zhejiang University","ror":"https://ror.org/05m1p5x56","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210166576"]},{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]},{"id":"https://openalex.org/I78577930","display_name":"Columbia University","ror":"https://ror.org/00hj8s172","country_code":"US","type":"education","lineage":["https://openalex.org/I78577930"]}],"countries":["CN","DE","US"],"is_corresponding":false,"raw_author_name":"Ruhong Zhou","raw_affiliation_strings":["College of Physics, College of Life Sciences, and Institute of Quantitative Biology, Zhejiang University , 866 Yuhangtang Road, Hangzhou 310058,","Department of Chemistry, Columbia University , New York, NY 10027 ,","Shanghai Institute for Advanced Study, Zhejiang University , 799 Dangui Road, Shanghai 201203,","The First Affiliated Hospital, School of Medicine, Zhejiang University , 866 Yuhangtang Road, Hangzhou 310058,"],"raw_orcid":"https://orcid.org/0000-0001-8624-5591","affiliations":[{"raw_affiliation_string":"College of Physics, College of Life Sciences, and Institute of Quantitative Biology, Zhejiang University , 866 Yuhangtang Road, Hangzhou 310058,","institution_ids":["https://openalex.org/I76130692"]},{"raw_affiliation_string":"Department of Chemistry, Columbia University , New York, NY 10027 ,","institution_ids":["https://openalex.org/I78577930"]},{"raw_affiliation_string":"Shanghai Institute for Advanced Study, Zhejiang University , 799 Dangui Road, Shanghai 201203,","institution_ids":["https://openalex.org/I4210137766"]},{"raw_affiliation_string":"The First Affiliated Hospital, School of Medicine, Zhejiang University , 866 Yuhangtang Road, Hangzhou 310058,","institution_ids":["https://openalex.org/I4210094450","https://openalex.org/I4210166576"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5059112910"],"corresponding_institution_ids":["https://openalex.org/I4210137766","https://openalex.org/I76130692"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.55567566,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"27","issue":"2","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.4618000090122223,"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"}},"topics":[{"id":"https://openalex.org/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.4618000090122223,"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/T10031","display_name":"T-cell and B-cell Immunology","score":0.296999990940094,"subfield":{"id":"https://openalex.org/subfields/2403","display_name":"Immunology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10580","display_name":"Immunotherapy and Immune Responses","score":0.10109999775886536,"subfield":{"id":"https://openalex.org/subfields/2403","display_name":"Immunology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/t-cell-receptor","display_name":"T-cell receptor","score":0.7919999957084656},{"id":"https://openalex.org/keywords/major-histocompatibility-complex","display_name":"Major histocompatibility complex","score":0.5637999773025513},{"id":"https://openalex.org/keywords/decoding-methods","display_name":"Decoding methods","score":0.5566999912261963},{"id":"https://openalex.org/keywords/encode","display_name":"ENCODE","score":0.48170000314712524},{"id":"https://openalex.org/keywords/generalizability-theory","display_name":"Generalizability theory","score":0.44609999656677246},{"id":"https://openalex.org/keywords/acquired-immune-system","display_name":"Acquired immune system","score":0.365200012922287},{"id":"https://openalex.org/keywords/robustness","display_name":"Robustness (evolution)","score":0.35760000348091125},{"id":"https://openalex.org/keywords/human-leukocyte-antigen","display_name":"Human leukocyte antigen","score":0.352400004863739}],"concepts":[{"id":"https://openalex.org/C19317047","wikidata":"https://www.wikidata.org/wiki/Q412037","display_name":"T-cell receptor","level":4,"score":0.7919999957084656},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5856000185012817},{"id":"https://openalex.org/C207936829","wikidata":"https://www.wikidata.org/wiki/Q423163","display_name":"Major histocompatibility complex","level":3,"score":0.5637999773025513},{"id":"https://openalex.org/C57273362","wikidata":"https://www.wikidata.org/wiki/Q576722","display_name":"Decoding methods","level":2,"score":0.5566999912261963},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5095000267028809},{"id":"https://openalex.org/C66746571","wikidata":"https://www.wikidata.org/wiki/Q1134833","display_name":"ENCODE","level":3,"score":0.48170000314712524},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4542999863624573},{"id":"https://openalex.org/C27158222","wikidata":"https://www.wikidata.org/wiki/Q5532422","display_name":"Generalizability theory","level":2,"score":0.44609999656677246},{"id":"https://openalex.org/C193419808","wikidata":"https://www.wikidata.org/wiki/Q1645075","display_name":"Acquired immune system","level":3,"score":0.365200012922287},{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.35760000348091125},{"id":"https://openalex.org/C188280979","wikidata":"https://www.wikidata.org/wiki/Q911125","display_name":"Human leukocyte antigen","level":3,"score":0.352400004863739},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.3264999985694885},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.30390000343322754},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.3034000098705292},{"id":"https://openalex.org/C155846161","wikidata":"https://www.wikidata.org/wiki/Q1143367","display_name":"Graphical model","level":2,"score":0.3003999888896942},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.3000999987125397},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.29499998688697815},{"id":"https://openalex.org/C147483822","wikidata":"https://www.wikidata.org/wiki/Q103537","display_name":"Antigen","level":2,"score":0.29420000314712524},{"id":"https://openalex.org/C2776090121","wikidata":"https://www.wikidata.org/wiki/Q193529","display_name":"T cell","level":3,"score":0.2935999929904938},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.2922999858856201},{"id":"https://openalex.org/C3018252375","wikidata":"https://www.wikidata.org/wiki/Q1059","display_name":"Immune recognition","level":3,"score":0.29089999198913574},{"id":"https://openalex.org/C179303850","wikidata":"https://www.wikidata.org/wiki/Q4300362","display_name":"Molecular recognition","level":3,"score":0.28279998898506165},{"id":"https://openalex.org/C2780868878","wikidata":"https://www.wikidata.org/wiki/Q1660197","display_name":"Immunogenicity","level":3,"score":0.2754000127315521}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D015789","descriptor_name":"HLA-A2 Antigen","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D015789","descriptor_name":"HLA-A2 Antigen","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D015789","descriptor_name":"HLA-A2 Antigen","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D015789","descriptor_name":"HLA-A2 Antigen","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbag048","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbag048","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:41834397","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41834397","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:12989321","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12989321/","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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbag048","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbag048","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1964083774","display_name":null,"funder_award_id":"2024YFA1307500","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G2130562261","display_name":null,"funder_award_id":"2024YFA1306400","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G2228442085","display_name":null,"funder_award_id":"U1967217","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3162117505","display_name":null,"funder_award_id":"SN-ZJU-SIAS-003","funder_id":"https://openalex.org/F4320322927","funder_display_name":"Zhejiang University"},{"id":"https://openalex.org/G5878354135","display_name":null,"funder_award_id":"2021YFA1201200","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program 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/F4320322927","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884"},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":56,"referenced_works":["https://openalex.org/W1896254721","https://openalex.org/W1951588750","https://openalex.org/W1975304761","https://openalex.org/W1979731533","https://openalex.org/W1983760021","https://openalex.org/W2029582401","https://openalex.org/W2038509173","https://openalex.org/W2049204549","https://openalex.org/W2061720803","https://openalex.org/W2066300055","https://openalex.org/W2076455712","https://openalex.org/W2081589596","https://openalex.org/W2105381977","https://openalex.org/W2105525514","https://openalex.org/W2111686340","https://openalex.org/W2130479394","https://openalex.org/W2134059200","https://openalex.org/W2134724359","https://openalex.org/W2146074801","https://openalex.org/W2155740919","https://openalex.org/W2163660115","https://openalex.org/W2165565773","https://openalex.org/W2177731497","https://openalex.org/W2275997631","https://openalex.org/W2290394493","https://openalex.org/W2360792712","https://openalex.org/W2558748708","https://openalex.org/W2623562434","https://openalex.org/W2728365508","https://openalex.org/W2759890769","https://openalex.org/W2762030706","https://openalex.org/W2797967938","https://openalex.org/W2800971266","https://openalex.org/W2992752586","https://openalex.org/W3094560178","https://openalex.org/W3116512470","https://openalex.org/W3202105508","https://openalex.org/W4206367183","https://openalex.org/W4220655797","https://openalex.org/W4229451133","https://openalex.org/W4293003482","https://openalex.org/W4310945495","https://openalex.org/W4321440624","https://openalex.org/W4323974789","https://openalex.org/W4360999048","https://openalex.org/W4367049161","https://openalex.org/W4386519564","https://openalex.org/W4387972659","https://openalex.org/W4388847467","https://openalex.org/W4389208185","https://openalex.org/W4389920712","https://openalex.org/W4400503324","https://openalex.org/W4401652414","https://openalex.org/W4404899980","https://openalex.org/W4406385470","https://openalex.org/W4407316423"],"related_works":[],"abstract_inverted_index":{"T":[0,188],"cell":[1,189],"receptor":[2,129],"(TCR)":[3],"recognition":[4,190],"of":[5,36,53,108,151],"peptide-major":[6],"histocompatibility":[7],"complex":[8],"(pMHC)":[9],"molecules":[10],"is":[11],"the":[12,39,50,66,149,157],"critical":[13,138],"first":[14],"step":[15],"in":[16,64,175],"adaptive":[17],"immune":[18],"activation,":[19],"shaping":[20],"immunity":[21],"against":[22],"pathogens":[23],"and":[24,56,85,89,122,141,170,191,202],"tumors,":[25],"as":[26,28],"well":[27],"tolerance":[29],"to":[30,104],"self.":[31],"Despite":[32],"extensive":[33],"structural":[34,59],"characterization":[35],"TCR-pMHC":[37,71],"complexes,":[38,163],"molecular":[40,177],"principles":[41],"underlying":[42],"this":[43],"process":[44],"remain":[45],"incompletely":[46],"understood,":[47],"hindered":[48],"by":[49,160],"inherent":[51],"duality":[52],"TCR":[54,101,119,152,166],"specificity":[55],"cross-reactivity.":[57],"Traditional":[58],"analyses":[60],"often":[61],"fall":[62],"short":[63],"capturing":[65],"multidimensional":[67],"features":[68,91],"that":[69,82,127],"govern":[70],"engagement.":[72,130],"Here,":[73],"we":[74,136],"introduce":[75],"a":[76,105,182,193],"multimodal":[77],"geometric":[78],"deep":[79],"learning":[80],"framework":[81],"systematically":[83],"extracts":[84],"learns":[86],"various":[87],"physicochemical":[88],"spatial":[90],"from":[92],"pMHC":[93],"interfaces,":[94],"which":[95],"encode":[96],"key":[97],"immunological":[98],"cues":[99],"for":[100,186,196],"recognition.":[102],"Applied":[103],"curated":[106],"dataset":[107],"human":[109],"leukocyte":[110],"antigens":[111],"HLA-A*02-peptide-TCR":[112],"crystal":[113],"structures,":[114],"our":[115],"model":[116],"robustly":[117],"predicts":[118],"binding":[120],"preferences":[121],"uncovers":[123],"interfacial":[124],"\"immunological":[125],"fingerprints\"":[126],"inform":[128],"Through":[131],"an":[132],"integrated":[133],"explainability":[134],"module,":[135],"identify":[137],"contact":[139],"residues":[140],"interaction":[142],"motifs,":[143],"thus":[144],"providing":[145],"interpretable":[146],"insights":[147],"into":[148],"determinants":[150],"specificity.":[153],"We":[154],"further":[155],"demonstrate":[156],"model's":[158],"generalizability":[159],"analyzing":[161],"HLA-B*27-peptide":[162],"revealing":[164],"potential":[165],"cross-reactivity":[167],"between":[168],"self-derived":[169],"bacterial":[171],"peptides-highlighting":[172],"its":[173],"utility":[174],"probing":[176],"mimicry.":[178],"This":[179],"work":[180],"establishes":[181],"scalable,":[183],"structure-based":[184],"approach":[185],"decoding":[187],"offers":[192],"powerful":[194],"tool":[195],"guiding":[197],"antigen":[198],"design,":[199],"vaccine":[200],"development,":[201],"TCR-based":[203],"immunotherapies.":[204]},"counts_by_year":[],"updated_date":"2026-04-29T09:16:38.111599","created_date":"2026-03-17T00:00:00"}