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T-cell recognition relies on the sophisticated ternary interaction between the T-cell receptor (TCR), the major histocompatibility complex (MHC) molecule, and the peptide antigen, which forms the peptide\u2013MHC (pMHC) complex. Computational methods, particularly artificial intelligence (AI), are indispensable for accurately predicting these complex bindings. This review systematically surveys the rapidly evolving AI-driven landscape for T-cell antigen identification, providing a comprehensive categorization of methods for MHC-I, MHC-II, and the highly complex TCR\u2013pMHC binding prediction, alongside foundational data resources. Crucially, we conduct a rigorous, standardized benchmarking of 18 state-of-the-art TCR\u2013pMHC prediction models across diverse training data sources. Our evaluation on two distinct and challenging out-of-distribution (OOD) unseen epitope variant datasets reveals a significant and concerning generalization gap in current predictors. Notably, the overall absolute predictive gain remains marginal across all models under OOD conditions. This result underscores a severe and persistent generalization challenge when faced with novel epitope variants. To address these limitations, we emphasize the urgent need for enhanced structural modeling, the integration of multi-omics data, and the development of generative models for de novo TCR design. By advancing these computational frontiers, our community can accelerate the transition from prediction to rational design in immunoinformatics.<\/jats:p>","DOI":"10.1093\/bib\/bbag123","type":"journal-article","created":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T12:42:41Z","timestamp":1772109761000},"source":"Crossref","is-referenced-by-count":0,"title":["AI-driven computational methods and benchmarking for T-cell antigen identification"],"prefix":"10.1093","volume":"27","author":[{"given":"Yang","family":"Deng","sequence":"first","affiliation":[{"name":"Center for Bioinformatics, School of Life Science and Technology, Harbin Institute of Technology , 92 Xidazhi Street, Nangang District, Harbin, 150000 Heilongjiang Province,","place":["China"]}]},{"given":"Jinhao","family":"Que","sequence":"additional","affiliation":[{"name":"Center for Bioinformatics, School of Life Science and Technology, Harbin Institute of Technology , 92 Xidazhi Street, Nangang District, Harbin, 150000 Heilongjiang Province,","place":["China"]}]},{"given":"Guangfu","family":"Xue","sequence":"additional","affiliation":[{"name":"Center for Bioinformatics, School of Life Science and Technology, Harbin Institute of Technology , 92 Xidazhi Street, Nangang District, Harbin, 150000 Heilongjiang Province,","place":["China"]}]},{"given":"Yideng","family":"Cai","sequence":"additional","affiliation":[{"name":"Center for Bioinformatics, School of Life Science and Technology, Harbin Institute of Technology , 92 Xidazhi Street, Nangang District, Harbin, 150000 Heilongjiang Province,","place":["China"]}]},{"given":"Wenyi","family":"Yang","sequence":"additional","affiliation":[{"name":"Center for Bioinformatics, School of Life Science and Technology, Harbin Institute of Technology , 92 Xidazhi Street, Nangang District, Harbin, 150000 Heilongjiang Province,","place":["China"]}]},{"given":"Yilin","family":"Wang","sequence":"additional","affiliation":[{"name":"Center for Bioinformatics, School of Life Science and Technology, Harbin Institute of Technology , 92 Xidazhi Street, Nangang District, Harbin, 150000 Heilongjiang Province,","place":["China"]}]},{"given":"Yi","family":"Hui","sequence":"additional","affiliation":[{"name":"Center for Bioinformatics, School of Life Science and Technology, Harbin Institute of Technology , 92 Xidazhi Street, Nangang District, Harbin, 150000 Heilongjiang Province,","place":["China"]}]},{"given":"Zuxiang","family":"Wang","sequence":"additional","affiliation":[{"name":"School of Interdisciplinary Medicine and Engineering, Harbin Medical University , 157 Baojian Road, Nangang District, Harbin, 150076 Heilongjiang Province,","place":["China"]}]},{"given":"Yi","family":"Lin","sequence":"additional","affiliation":[{"name":"School of Interdisciplinary Medicine and Engineering, Harbin Medical University , 157 Baojian Road, Nangang District, Harbin, 150076 Heilongjiang Province,","place":["China"]}]},{"given":"Wenyang","family":"Zhou","sequence":"additional","affiliation":[{"name":"School of Interdisciplinary Medicine and Engineering, Harbin Medical University , 157 Baojian Road, Nangang District, Harbin, 150076 Heilongjiang Province,","place":["China"]}]},{"given":"Zhaochun","family":"Xu","sequence":"additional","affiliation":[{"name":"School of Interdisciplinary Medicine and Engineering, Harbin Medical University , 157 Baojian Road, Nangang District, Harbin, 150076 Heilongjiang Province,","place":["China"]}]},{"given":"Qinghua","family":"Jiang","sequence":"additional","affiliation":[{"name":"Center for Bioinformatics, School of Life Science and Technology, Harbin Institute of Technology , 92 Xidazhi Street, Nangang District, Harbin, 150000 Heilongjiang Province,","place":["China"]},{"name":"School of Interdisciplinary Medicine and Engineering, Harbin Medical University , 157 Baojian Road, Nangang District, Harbin, 150076 Heilongjiang Province,","place":["China"]}]},{"given":"Haoxiu","family":"Sun","sequence":"additional","affiliation":[{"name":"School of Interdisciplinary Medicine and Engineering, Harbin Medical University , 157 Baojian Road, Nangang District, Harbin, 150076 Heilongjiang Province,","place":["China"]}]}],"member":"286","published-online":{"date-parts":[[2026,3,17]]},"reference":[{"key":"2026031706564295500_ref1","doi-asserted-by":"publisher","first-page":"261","DOI":"10.1038\/nrd.2017.243","article-title":"mRNA vaccines \u2014 a new era in vaccinology","volume":"17","author":"Pardi","year":"2018","journal-title":"Nat Rev Drug Discov"},{"key":"2026031706564295500_ref2","doi-asserted-by":"publisher","first-page":"1446","DOI":"10.7150\/ijbs.59233","article-title":"mRNA vaccines for COVID-19: what, why and how","volume":"17","author":"Park","year":"2021","journal-title":"Int J Biol 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