{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,16]],"date-time":"2026-06-16T07:02:13Z","timestamp":1781593333363,"version":"3.54.5"},"reference-count":45,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2023,5,4]],"date-time":"2023-05-04T00:00:00Z","timestamp":1683158400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["GM144083"],"award-info":[{"award-number":["GM144083"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001807","name":"S\u00e3o Paulo Research Foundation","doi-asserted-by":"publisher","award":["#2022\/04260-6"],"award-info":[{"award-number":["#2022\/04260-6"]}],"id":[{"id":"10.13039\/501100001807","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,7,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The cellular immune system, which is a critical component of human immunity, uses T\u00a0cell receptors (TCRs) to recognize antigenic proteins in the form of peptides presented by major histocompatibility complex (MHC) proteins. Accurate definition of the structural basis of TCRs and their engagement of peptide\u2013MHCs can provide major insights into normal and aberrant immunity, and can help guide the design of vaccines and immunotherapeutics. Given the limited amount of experimentally determined TCR\u2013peptide\u2013MHC structures and the vast amount of TCRs within each individual as well as antigenic targets, accurate computational modeling approaches are needed. Here, we report a major update to our web server, TCRmodel, which was originally developed to model unbound TCRs from sequence, to now model TCR\u2013peptide\u2013MHC complexes from sequence, utilizing several adaptations of AlphaFold. This method, named TCRmodel2, allows users to submit sequences through an easy-to-use interface and shows similar or greater accuracy than AlphaFold and other methods to model TCR\u2013peptide\u2013MHC complexes based on benchmarking. It can generate models of complexes in 15\u00a0minutes, and output models are provided with confidence scores and an integrated molecular viewer. TCRmodel2 is available at\u00a0https:\/\/tcrmodel.ibbr.umd.edu.<\/jats:p>","DOI":"10.1093\/nar\/gkad356","type":"journal-article","created":{"date-parts":[[2023,5,4]],"date-time":"2023-05-04T12:25:52Z","timestamp":1683203152000},"page":"W569-W576","source":"Crossref","is-referenced-by-count":97,"title":["TCRmodel2: high-resolution modeling of T\u00a0cell receptor recognition using deep learning"],"prefix":"10.1093","volume":"51","author":[{"given":"Rui","family":"Yin","sequence":"first","affiliation":[{"name":"University of Maryland Institute for Bioscience and Biotechnology Research , Rockville , MD \u00a020850, USA"},{"name":"Department of Cell Biology and Molecular Genetics, University of Maryland , College Park , MD \u00a020742, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Helder V","family":"Ribeiro-Filho","sequence":"additional","affiliation":[{"name":"University of Maryland Institute for Bioscience and Biotechnology Research , Rockville , MD \u00a020850, USA"},{"name":"Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials , Campinas \u00a013083-100, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Valerie","family":"Lin","sequence":"additional","affiliation":[{"name":"University of Maryland Institute for Bioscience and Biotechnology Research , Rockville , MD \u00a020850, USA"},{"name":"Thomas S. Wootton High School , Rockville , MD \u00a020850, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ragul","family":"Gowthaman","sequence":"additional","affiliation":[{"name":"University of Maryland Institute for Bioscience and Biotechnology Research , Rockville , MD \u00a020850, USA"},{"name":"Department of Cell Biology and Molecular Genetics, University of Maryland , College Park , MD \u00a020742, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Melyssa","family":"Cheung","sequence":"additional","affiliation":[{"name":"University of Maryland Institute for Bioscience and Biotechnology Research , Rockville , MD \u00a020850, USA"},{"name":"Department of Chemistry and Biochemistry, University of Maryland , College Park , MD \u00a020742, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4821-0368","authenticated-orcid":false,"given":"Brian\u00a0G","family":"Pierce","sequence":"additional","affiliation":[{"name":"University of Maryland Institute for Bioscience and Biotechnology Research , Rockville , MD \u00a020850, USA"},{"name":"Department of Cell Biology and Molecular Genetics, University of Maryland , College Park , MD \u00a020742, USA"},{"name":"University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center , Baltimore , MD \u00a021201, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2023,5,4]]},"reference":[{"key":"2023070504590801100_B1","volume-title":"Immunobiology: The Immune System in Health and Disease","author":"Janeway","year":"2005","edition":"6th edn"},{"key":"2023070504590801100_B2","doi-asserted-by":"crossref","first-page":"186","DOI":"10.1038\/s41590-021-01122-w","article-title":"The T cell immune response against SARS-CoV-2","volume":"23","author":"Moss","year":"2022","journal-title":"Nat. Immunol."},{"key":"2023070504590801100_B3","doi-asserted-by":"crossref","first-page":"32","DOI":"10.1111\/imr.12002","article-title":"Structural basis for self-recognition by autoimmune T-cell receptors","volume":"250","author":"Yin","year":"2012","journal-title":"Immunol. Rev."},{"key":"2023070504590801100_B4","doi-asserted-by":"crossref","first-page":"771","DOI":"10.1038\/s41586-022-05501-7","article-title":"Autoimmunity-associated T cell receptors recognize HLA-B*27-bound peptides","volume":"612","author":"Yang","year":"2022","journal-title":"Nature"},{"key":"2023070504590801100_B5","doi-asserted-by":"crossref","first-page":"2255","DOI":"10.1056\/NEJMoa1609279","article-title":"T-cell transfer therapy targeting mutant KRAS in cancer","volume":"375","author":"Tran","year":"2016","journal-title":"N. Engl. J. Med."},{"key":"2023070504590801100_B6","doi-asserted-by":"crossref","first-page":"724","DOI":"10.1038\/s41591-018-0040-8","article-title":"Immune recognition of somatic mutations leading to complete durable regression in metastatic breast cancer","volume":"24","author":"Zacharakis","year":"2018","journal-title":"Nat. Med."},{"key":"2023070504590801100_B7","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1016\/j.ctrv.2019.06.001","article-title":"Novel TCR-based biologics: mobilising T cells to warm \u2018cold\u2019 tumours","volume":"77","author":"Lowe","year":"2019","journal-title":"Cancer Treat. Rev."},{"key":"2023070504590801100_B8","doi-asserted-by":"crossref","first-page":"395","DOI":"10.1038\/nsmb.3383","article-title":"Broad TCR repertoire and diverse structural solutions for recognition of an immunodominant CD8+ T cell epitope","volume":"24","author":"Song","year":"2017","journal-title":"Nat. Struct. Mol. Biol."},{"key":"2023070504590801100_B9","doi-asserted-by":"crossref","first-page":"18851","DOI":"10.1038\/srep18851","article-title":"Direct molecular mimicry enables off-target cardiovascular toxicity by an enhanced affinity TCR designed for cancer immunotherapy","volume":"6","author":"Raman","year":"2016","journal-title":"Sci. Rep."},{"key":"2023070504590801100_B10","doi-asserted-by":"crossref","first-page":"e1003478","DOI":"10.1371\/journal.pcbi.1003478","article-title":"Computational design of the affinity and specificity of a therapeutic T cell receptor","volume":"10","author":"Pierce","year":"2014","journal-title":"PLoS Comput. Biol."},{"key":"2023070504590801100_B11","doi-asserted-by":"crossref","first-page":"2587","DOI":"10.4049\/jimmunol.1302344","article-title":"Specific increase in potency via structure-based design of a TCR","volume":"193","author":"Malecek","year":"2014","journal-title":"J. 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