{"id":"https://openalex.org/W4406047234","doi":"https://doi.org/10.1109/tcbbio.2024.3504235","title":"TCR-pMHC Binding Specificity Prediction From Structure Using Graph Neural Networks","display_name":"TCR-pMHC Binding Specificity Prediction From Structure Using Graph Neural Networks","publication_year":2025,"publication_date":"2025-01-01","ids":{"openalex":"https://openalex.org/W4406047234","doi":"https://doi.org/10.1109/tcbbio.2024.3504235","pmid":"https://pubmed.ncbi.nlm.nih.gov/40811222"},"language":"en","primary_location":{"id":"doi:10.1109/tcbbio.2024.3504235","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2024.3504235","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043","2998-4165"],"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 Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12356035/pdf/nihms-2054937.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5091822104","display_name":"Jared K. Slone","orcid":"https://orcid.org/0000-0002-6629-4166"},"institutions":[{"id":"https://openalex.org/I74775410","display_name":"Rice University","ror":"https://ror.org/008zs3103","country_code":"US","type":"education","lineage":["https://openalex.org/I74775410"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jared K. Slone","raw_affiliation_strings":["Department of Computer Science, Rice University, Houston, TX, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Rice University, Houston, TX, USA","institution_ids":["https://openalex.org/I74775410"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066354975","display_name":"Anja Conev","orcid":"https://orcid.org/0000-0001-9049-0266"},"institutions":[{"id":"https://openalex.org/I74775410","display_name":"Rice University","ror":"https://ror.org/008zs3103","country_code":"US","type":"education","lineage":["https://openalex.org/I74775410"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Anja Conev","raw_affiliation_strings":["Department of Computer Science, Rice University, Houston, TX, USA"],"raw_orcid":"https://orcid.org/0000-0001-9049-0266","affiliations":[{"raw_affiliation_string":"Department of Computer Science, Rice University, Houston, TX, USA","institution_ids":["https://openalex.org/I74775410"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034774826","display_name":"Maur\u00edcio Rigo","orcid":"https://orcid.org/0000-0002-1584-6194"},"institutions":[{"id":"https://openalex.org/I74775410","display_name":"Rice University","ror":"https://ror.org/008zs3103","country_code":"US","type":"education","lineage":["https://openalex.org/I74775410"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mauricio M. Rigo","raw_affiliation_strings":["Department of Computer Science, Rice University, Houston, TX, USA"],"raw_orcid":"https://orcid.org/0000-0002-1584-6194","affiliations":[{"raw_affiliation_string":"Department of Computer Science, Rice University, Houston, TX, USA","institution_ids":["https://openalex.org/I74775410"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088889988","display_name":"Alexandre Reuben","orcid":"https://orcid.org/0000-0003-4510-0382"},"institutions":[{"id":"https://openalex.org/I1343551460","display_name":"The University of Texas MD Anderson Cancer Center","ror":"https://ror.org/04twxam07","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1343551460"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alexandre Reuben","raw_affiliation_strings":["Department of Thoracic/Head &amp; Neck Medical Oncology, MD Anderson Cancer Center, Houston, TX, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Thoracic/Head &amp; Neck Medical Oncology, MD Anderson Cancer Center, Houston, TX, USA","institution_ids":["https://openalex.org/I1343551460"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5067205988","display_name":"Lydia E. Kavraki","orcid":"https://orcid.org/0000-0003-0699-8038"},"institutions":[{"id":"https://openalex.org/I74775410","display_name":"Rice University","ror":"https://ror.org/008zs3103","country_code":"US","type":"education","lineage":["https://openalex.org/I74775410"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lydia E. Kavraki","raw_affiliation_strings":["Department of Computer Science, Rice University, Houston, TX, USA","Ken Kennedy Institute, Houston, TX, USA"],"raw_orcid":"https://orcid.org/0000-0003-0699-8038","affiliations":[{"raw_affiliation_string":"Department of Computer Science, Rice University, Houston, TX, USA","institution_ids":["https://openalex.org/I74775410"]},{"raw_affiliation_string":"Ken Kennedy Institute, Houston, TX, USA","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":2645,"currency":"USD","value_usd":2645},"apc_paid":null,"fwci":8.5531,"has_fulltext":true,"cited_by_count":13,"citation_normalized_percentile":{"value":0.97835566,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":99},"biblio":{"volume":"22","issue":"1","first_page":"171","last_page":"179"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.998199999332428,"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":0.998199999332428,"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/T11948","display_name":"Machine Learning in Materials Science","score":0.9869999885559082,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9681000113487244,"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/computer-science","display_name":"Computer science","score":0.5006766319274902},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.4717089831829071},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.431751012802124},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4255129098892212},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3410891592502594},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.19788625836372375},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.18508315086364746}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5006766319274902},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4717089831829071},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.431751012802124},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4255129098892212},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3410891592502594},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.19788625836372375},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.18508315086364746}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1109/tcbbio.2024.3504235","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2024.3504235","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043","2998-4165"],"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 Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40811222","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40811222","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":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12356035","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12356035/","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12356035/pdf/nihms-2054937.pdf","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"IEEE Trans Comput Biol Bioinform","raw_type":"Text"},{"id":"pmh:oai:europepmc.org:11563447","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12356035","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:12356035","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12356035/","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12356035/pdf/nihms-2054937.pdf","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"IEEE Trans Comput Biol Bioinform","raw_type":"Text"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1960506700","display_name":"PROTEAN-CR: Proteomics Toolkit for Ensemble Analysis in Cancer Research","funder_award_id":"5u01ca258512-03","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G2640905883","display_name":null,"funder_award_id":"T15LM007093","funder_id":"https://openalex.org/F4320337372","funder_display_name":"U.S. National Library of Medicine"},{"id":"https://openalex.org/G5287771122","display_name":null,"funder_award_id":"5T15LM007093","funder_id":"https://openalex.org/F4320337372","funder_display_name":"U.S. National Library of Medicine"},{"id":"https://openalex.org/G8946597769","display_name":null,"funder_award_id":"U01 CA258512","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G902374612","display_name":null,"funder_award_id":"R21 CA283852","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320306078","display_name":"U.S. Department of Defense","ror":"https://ror.org/0447fe631"},{"id":"https://openalex.org/F4320306997","display_name":"LUNGevity Foundation","ror":"https://ror.org/02t0s0z58"},{"id":"https://openalex.org/F4320308129","display_name":"Cancer Prevention and Research Institute of Texas","ror":"https://ror.org/0003xa228"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320332521","display_name":"University of Texas MD Anderson Cancer Center","ror":"https://ror.org/04twxam07"},{"id":"https://openalex.org/F4320337191","display_name":"Research Institute for Microbial Diseases, Osaka University","ror":null},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"},{"id":"https://openalex.org/F4320337372","display_name":"U.S. National Library of Medicine","ror":"https://ror.org/0060t0j89"},{"id":"https://openalex.org/F5644061488","display_name":"Troper Wojcicki Foundation","ror":"https://ror.org/03bmwhc32"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4406047234.pdf","grobid_xml":"https://content.openalex.org/works/W4406047234.grobid-xml"},"referenced_works_count":70,"referenced_works":["https://openalex.org/W1857461391","https://openalex.org/W1967195968","https://openalex.org/W1983412131","https://openalex.org/W2021945571","https://openalex.org/W2053707749","https://openalex.org/W2084965322","https://openalex.org/W2116863267","https://openalex.org/W2144185370","https://openalex.org/W2613978126","https://openalex.org/W2752126733","https://openalex.org/W2762030706","https://openalex.org/W2766169371","https://openalex.org/W2766856748","https://openalex.org/W2894849296","https://openalex.org/W2932935282","https://openalex.org/W2973294922","https://openalex.org/W2979326653","https://openalex.org/W2990308980","https://openalex.org/W3020331344","https://openalex.org/W3043056436","https://openalex.org/W3080758869","https://openalex.org/W3085380432","https://openalex.org/W3113525558","https://openalex.org/W3135351475","https://openalex.org/W3160101264","https://openalex.org/W3163602801","https://openalex.org/W3164277106","https://openalex.org/W3177828909","https://openalex.org/W3183967699","https://openalex.org/W3187966659","https://openalex.org/W3197675872","https://openalex.org/W3197908803","https://openalex.org/W3198396294","https://openalex.org/W3198942356","https://openalex.org/W4210547400","https://openalex.org/W4220974185","https://openalex.org/W4247367216","https://openalex.org/W4280617006","https://openalex.org/W4282917061","https://openalex.org/W4283397333","https://openalex.org/W4286631898","https://openalex.org/W4308584245","https://openalex.org/W4311619464","https://openalex.org/W4313585433","https://openalex.org/W4317532687","https://openalex.org/W4319455163","https://openalex.org/W4323320132","https://openalex.org/W4327573630","https://openalex.org/W4366272177","https://openalex.org/W4366816229","https://openalex.org/W4367049975","https://openalex.org/W4368357399","https://openalex.org/W4380264494","https://openalex.org/W4380739447","https://openalex.org/W4380882762","https://openalex.org/W4386161992","https://openalex.org/W4387037681","https://openalex.org/W4388901968","https://openalex.org/W4389262331","https://openalex.org/W4389304119","https://openalex.org/W4391472665","https://openalex.org/W6631943919","https://openalex.org/W6639001298","https://openalex.org/W6734194636","https://openalex.org/W6736685754","https://openalex.org/W6755184371","https://openalex.org/W6783213970","https://openalex.org/W6797464607","https://openalex.org/W6803919185","https://openalex.org/W6858684905"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052"],"abstract_inverted_index":{"The":[0],"mapping":[1],"of":[2,57,85,100,108],"T-cell-receptors":[3],"(TCRs)":[4],"to":[5,11,25,45,80,123,129],"their":[6],"cognate":[7],"peptides":[8],"is":[9],"crucial":[10],"improving":[12],"cancer":[13],"immunotherapy.":[14],"Numerous":[15],"computational":[16],"methods":[17,170],"and":[18,60,68,88,103,127,175],"machine":[19,147],"learning":[20,148],"tools":[21],"have":[22,73],"been":[23],"proposed":[24],"aid":[26],"in":[27,65,69,96],"the":[28,53,58,77,82,97,101],"task.":[29],"Yet,":[30],"accurately":[31],"constructing":[32],"this":[33],"map":[34],"computationally":[35],"remains":[36],"a":[37,144],"difficult":[38],"problem.":[39],"Most":[40],"prior":[41],"work":[42],"has":[43],"sought":[44],"predict":[46],"TCR-peptide-MHC":[47],"(TCR-pMHC)":[48],"binding":[49,136,153],"specificity":[50,110,154],"by":[51,115],"analyzing":[52],"amino":[54],"acid":[55],"sequences":[56],"TCRs":[59,102],"peptides.":[61],"However,":[62],"recent":[63],"advancements":[64],"crystallography,":[66],"cryo-EM,":[67],"silico":[70],"protein":[71,119,180],"modeling":[72],"provided":[74],"researchers":[75],"with":[76],"necessary":[78],"data":[79,121],"analyze":[81],"3D":[83,98,156],"structures":[84],"TCRs,":[86],"peptides,":[87],"MHCs.":[89],"Current":[90],"research":[91],"suggests":[92],"that":[93,111,161],"information":[94],"contained":[95],"structure":[99,120,157],"pMHCs":[104],"can":[105],"explain":[106],"instances":[107],"TCR":[109],"are":[112],"not":[113],"explained":[114],"sequence":[116],"alone.":[117],"As":[118],"continues":[122],"become":[124,138],"more":[125],"accurate":[126],"easier":[128],"obtain,":[130],"structure-based":[131],"methodologies":[132],"for":[133,150],"predicting":[134,151],"TCR-pMHC":[135,152],"will":[137],"increasingly":[139],"important.":[140],"We":[141,159],"present":[142],"STAG,":[143],"novel":[145],"graph-based":[146],"architecture":[149],"using":[155],"data.":[158],"show":[160],"STAG":[162],"achieves":[163],"comparable":[164],"or":[165],"better":[166],"performance":[167],"than":[168],"existing":[169],"while":[171],"utilizing":[172],"only":[173],"spatial":[174],"physicochemical":[176],"features":[177],"from":[178],"modeled":[179],"structures.":[181]},"counts_by_year":[{"year":2026,"cited_by_count":6},{"year":2025,"cited_by_count":7}],"updated_date":"2026-08-29T07:29:34.045763","created_date":"2025-10-10T00:00:00"}
