{"id":"https://openalex.org/W4417116839","doi":"https://doi.org/10.1093/bib/bbag289","title":"Benchmarking TCR\u2013pMHC structure prediction: a unified evaluation and CDR3-based functional insights","display_name":"Benchmarking TCR\u2013pMHC structure prediction: a unified evaluation and CDR3-based functional insights","publication_year":2026,"publication_date":"2026-05-01","ids":{"openalex":"https://openalex.org/W4417116839","doi":"https://doi.org/10.1093/bib/bbag289","pmid":"https://pubmed.ncbi.nlm.nih.gov/42248582"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbag289","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbag289","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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/bbag289","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5109620353","display_name":"J D Lu","orcid":"https://orcid.org/0009-0002-9804-0651"},"institutions":[{"id":"https://openalex.org/I143868143","display_name":"Anhui University","ror":"https://ror.org/05th6yx34","country_code":"CN","type":"education","lineage":["https://openalex.org/I143868143"]},{"id":"https://openalex.org/I4210161752","display_name":"Beijing Haidian Hospital","ror":"https://ror.org/058x5eq06","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210161752"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jiadong Lu","raw_affiliation_strings":["School of Artificial Intelligence and Data Science, University of Science and Technology of China , Huangshan Road, Shushan District, Hefei 230027, Anhui ,","Zhongguancun Academy , No. 17, Second Ring Road, Daniufang, Haidian District, Beijing 100094 ,"],"raw_orcid":"https://orcid.org/0009-0002-9804-0651","affiliations":[{"raw_affiliation_string":"School of Artificial Intelligence and Data Science, University of Science and Technology of China , Huangshan Road, Shushan District, Hefei 230027, Anhui ,","institution_ids":["https://openalex.org/I143868143"]},{"raw_affiliation_string":"Zhongguancun Academy , No. 17, Second Ring Road, Daniufang, Haidian District, Beijing 100094 ,","institution_ids":["https://openalex.org/I4210161752"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014616952","display_name":"Xinyuan Zhu","orcid":"https://orcid.org/0000-0002-2891-837X"},"institutions":[{"id":"https://openalex.org/I126520041","display_name":"University of Science and Technology of China","ror":"https://ror.org/04c4dkn09","country_code":"CN","type":"education","lineage":["https://openalex.org/I126520041","https://openalex.org/I19820366"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xinyuan Zhu","raw_affiliation_strings":["School of Information Science and Technology, University of Science and Technology of China , Huangshan Road, Shushan District, Hefei 230027, Anhui ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Information Science and Technology, University of Science and Technology of China , Huangshan Road, Shushan District, Hefei 230027, Anhui ,","institution_ids":["https://openalex.org/I126520041"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001984245","display_name":"Xinting Hu","orcid":"https://orcid.org/0000-0003-0305-3653"},"institutions":[{"id":"https://openalex.org/I143868143","display_name":"Anhui University","ror":"https://ror.org/05th6yx34","country_code":"CN","type":"education","lineage":["https://openalex.org/I143868143"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xinting Hu","raw_affiliation_strings":["School of Artificial Intelligence and Data Science, University of Science and Technology of China , Huangshan Road, Shushan District, Hefei 230027, Anhui ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Artificial Intelligence and Data Science, University of Science and Technology of China , Huangshan Road, Shushan District, Hefei 230027, Anhui ,","institution_ids":["https://openalex.org/I143868143"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100439655","display_name":"Cheng Zhang","orcid":"https://orcid.org/0000-0002-7196-9463"},"institutions":[{"id":"https://openalex.org/I139024713","display_name":"Guangdong University of Technology","ror":"https://ror.org/04azbjn80","country_code":"CN","type":"education","lineage":["https://openalex.org/I139024713"]},{"id":"https://openalex.org/I889458895","display_name":"University of Hong Kong","ror":"https://ror.org/02zhqgq86","country_code":"HK","type":"education","lineage":["https://openalex.org/I889458895"]}],"countries":["CN","HK"],"is_corresponding":false,"raw_author_name":"Cheng Zhang","raw_affiliation_strings":["Bioscience and Biomedical Engineering Thrust, The Hong Kong University of Science and Technology (Guangzhou) , Duxue Road, Nansha District, Guangzhou 511458, Guangdong ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioscience and Biomedical Engineering Thrust, The Hong Kong University of Science and Technology (Guangzhou) , Duxue Road, Nansha District, Guangzhou 511458, Guangdong ,","institution_ids":["https://openalex.org/I139024713","https://openalex.org/I889458895"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5051925942","display_name":"Fuli Feng","orcid":"https://orcid.org/0000-0002-5828-9842"},"institutions":[{"id":"https://openalex.org/I143868143","display_name":"Anhui University","ror":"https://ror.org/05th6yx34","country_code":"CN","type":"education","lineage":["https://openalex.org/I143868143"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Fuli Feng","raw_affiliation_strings":["School of Artificial Intelligence and Data Science, University of Science and Technology of China , Huangshan Road, Shushan District, Hefei 230027, Anhui ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Artificial Intelligence and Data Science, University of Science and Technology of China , Huangshan Road, Shushan District, Hefei 230027, Anhui ,","institution_ids":["https://openalex.org/I143868143"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":4.3846,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.87169209,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":97},"biblio":{"volume":"27","issue":"3","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":0.5303999781608582,"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":0.5303999781608582,"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":0.26899999380111694,"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/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":0.0340999998152256,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/benchmarking","display_name":"Benchmarking","score":0.7983999848365784},{"id":"https://openalex.org/keywords/correctness","display_name":"Correctness","score":0.6862000226974487},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.5539000034332275},{"id":"https://openalex.org/keywords/quality","display_name":"Quality (philosophy)","score":0.3456999957561493},{"id":"https://openalex.org/keywords/predictive-modelling","display_name":"Predictive modelling","score":0.3125},{"id":"https://openalex.org/keywords/docking","display_name":"Docking (animal)","score":0.30559998750686646}],"concepts":[{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.7983999848365784},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6881999969482422},{"id":"https://openalex.org/C55439883","wikidata":"https://www.wikidata.org/wiki/Q360812","display_name":"Correctness","level":2,"score":0.6862000226974487},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.5539000034332275},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.45500001311302185},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4462999999523163},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4133000075817108},{"id":"https://openalex.org/C2779530757","wikidata":"https://www.wikidata.org/wiki/Q1207505","display_name":"Quality (philosophy)","level":2,"score":0.3456999957561493},{"id":"https://openalex.org/C45804977","wikidata":"https://www.wikidata.org/wiki/Q7239673","display_name":"Predictive modelling","level":2,"score":0.3125},{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.30559998750686646},{"id":"https://openalex.org/C61797465","wikidata":"https://www.wikidata.org/wiki/Q1188986","display_name":"Term (time)","level":2,"score":0.2930999994277954},{"id":"https://openalex.org/C67186912","wikidata":"https://www.wikidata.org/wiki/Q367664","display_name":"Data modeling","level":2,"score":0.27730000019073486},{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.2727000117301941},{"id":"https://openalex.org/C66024118","wikidata":"https://www.wikidata.org/wiki/Q1122506","display_name":"Computational model","level":2,"score":0.2630999982357025}],"mesh":[{"descriptor_ui":"D000095763","descriptor_name":"Immunoinformatics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000095763","descriptor_name":"Immunoinformatics","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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008285","descriptor_name":"Major Histocompatibility Complex","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008285","descriptor_name":"Major Histocompatibility Complex","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D022801","descriptor_name":"Complementarity Determining Regions","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D022801","descriptor_name":"Complementarity Determining Regions","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bib/bbag289","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbag289","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"doi:10.64898/2025.11.30.691400","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2025.11.30.691400","pdf_url":null,"source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},{"id":"pmid:42248582","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/42248582","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:13240595","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13240595/","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","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbag289","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbag289","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":44,"referenced_works":["https://openalex.org/W2000840258","https://openalex.org/W2049204549","https://openalex.org/W2063184115","https://openalex.org/W2115540209","https://openalex.org/W2155740919","https://openalex.org/W2161151688","https://openalex.org/W2165531467","https://openalex.org/W2508425869","https://openalex.org/W2904572271","https://openalex.org/W2949635314","https://openalex.org/W2950954328","https://openalex.org/W2951149542","https://openalex.org/W2953103783","https://openalex.org/W2955439997","https://openalex.org/W2968781851","https://openalex.org/W3015438624","https://openalex.org/W3177828909","https://openalex.org/W3186381913","https://openalex.org/W3198942356","https://openalex.org/W3202105508","https://openalex.org/W4220887281","https://openalex.org/W4281708617","https://openalex.org/W4281790889","https://openalex.org/W4285392187","https://openalex.org/W4286669150","https://openalex.org/W4292238158","https://openalex.org/W4323320132","https://openalex.org/W4327550249","https://openalex.org/W4360999048","https://openalex.org/W4368357399","https://openalex.org/W4376128352","https://openalex.org/W4378212112","https://openalex.org/W4382789897","https://openalex.org/W4385387090","https://openalex.org/W4389568864","https://openalex.org/W4392883366","https://openalex.org/W4395041526","https://openalex.org/W4399731408","https://openalex.org/W4400231442","https://openalex.org/W4400503324","https://openalex.org/W4401725571","https://openalex.org/W4402801121","https://openalex.org/W4402925967","https://openalex.org/W4406714966"],"related_works":[],"abstract_inverted_index":{"Interactions":[0],"between":[1],"T":[2],"cell":[3],"receptors":[4],"(TCRs)":[5],"and":[6,60,66,74,108,122,144],"peptide-major":[7],"histocompatibility":[8],"complexes":[9,59],"(pMHCs)":[10],"are":[11],"central":[12],"to":[13,37,115],"adaptive":[14],"immunity.":[15],"Recent":[16],"advances":[17],"in":[18,41,127],"structure":[19,53,141],"prediction":[20,54,142],"tools":[21],"have":[22],"enabled":[23],"atomic-level":[24],"modeling":[25,72],"of":[26,32,51,77,87,95,104,129,139,148],"TCR-pMHC":[27,52],"interactions.":[28],"However,":[29],"the":[30,70,85,92,96,136,146],"lack":[31],"systematic":[33],"evaluation":[34],"forces":[35],"practitioners":[36],"invest":[38],"substantial":[39],"resources":[40],"selecting":[42],"appropriate":[43],"tools.":[44],"Here,":[45],"we":[46,90],"present":[47],"a":[48],"comprehensive":[49],"benchmark":[50],"with":[55],"70":[56],"previously":[57],"unseen":[58],"13":[61],"models":[62,143],"spanning":[63],"MSA-based,":[64],"PLM-based,":[65],"docking-based":[67],"approaches,":[68],"revealing":[69],"superior":[71],"accuracy":[73],"docking":[75],"quality":[76],"MSA-based":[78],"methods,":[79],"especially":[80],"AlphaFold3.":[81],"To":[82],"further":[83],"enhance":[84],"utility":[86],"AlphaFold3":[88],"predictions,":[89],"identify":[91],"pLDDT":[93],"score":[94],"TCR":[97],"CDR3":[98],"region":[99],"as":[100],"an":[101],"informative":[102],"indicator":[103],"both":[105],"structural":[106],"correctness":[107],"functional":[109],"relevance.":[110],"Specifically,":[111],"it":[112],"enables":[113],"up":[114],"4.3%":[116],"Top-1":[117],"success":[118],"gain":[119],"through":[120],"reranking":[121],"captures":[123],"mutation-induced":[124],"affinity":[125],"changes":[126],"75.3%":[128],"cases.":[130],"Overall,":[131],"our":[132],"analysis":[133],"would":[134],"facilitate":[135],"practical":[137],"usage":[138],"immune":[140],"guide":[145],"advancement":[147],"these":[149],"models.":[150]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-07-16T13:24:37.021932","created_date":"2025-12-08T00:00:00"}
