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Despite its importance to the immune response, T-cell cross-reactivity poses a major challenge for the development of novel T cell\u2013based therapies. In this study, we present MHCXGraph, a graph-based computational approach for identifying conserved and immunologically relevant regions across multiple structures of peptides bound to MHC molecules (pMHC). Our approach provides three operational modes: Multiple, Pairwise, and Screening, with user-defined parameters, allowing flexible configuration according to specific scientific needs while delivering fully interpretable results through user-friendly interfaces. We evaluated MHCXGraph across several case studies, including peptides bound to classical MHC Class I, MHC Class II, unbound human leukocyte antigen (HLA) alleles, and pMHCs containing noncanonical amino acids, demonstrating its ability to capture conserved structural determinants beyond sequence similarity. By integrating structural information with efficient graph-based analysis, MHCXGraph addresses key limitations of sequence-based methods while maintaining computational scalability. Collectively, these results indicate that MHCXGraph can be readily integrated into computational pipelines for T-cell cross-reactivity discovery, especially in the context of $\\textit{de novo}$ pMHC engager design and T cell\u2013based vaccine development.<\/jats:p>","DOI":"10.1093\/bib\/bbag555","type":"journal-article","created":{"date-parts":[[2026,9,23]],"date-time":"2026-09-23T11:49:51Z","timestamp":1790164191000},"source":"Crossref","is-referenced-by-count":0,"title":["MHCXGraph: a graph-based approach to detecting T-cell receptor cross-reactivity"],"prefix":"10.1093","volume":"27","author":[{"ORCID":"https:\/\/orcid.org\/0009-0003-8978-3143","authenticated-orcid":false,"given":"Carlos D M S","family":"Sim\u00f5es","sequence":"first","affiliation":[{"name":"Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM) , Rua Giuseppe M\u00e1ximo Scolfaro, 10000, Polo II de Alta Tecnologia, Campinas, SP, 13083-100 ,","place":["Brazil"]},{"name":"Faculty of Pharmaceutical Sciences, University of Campinas (UNICAMP) , Rua Candido Portinari, 200, Cidade Universit\u00e1ria Zeferino Vaz, Campinas, SP, 13083-871 ,","place":["Brazil"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3971-6447","authenticated-orcid":false,"given":"Roc\u00edo L B R","family":"Maidana","sequence":"additional","affiliation":[{"name":"Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM) , Rua Giuseppe M\u00e1ximo Scolfaro, 10000, Polo II de Alta Tecnologia, Campinas, SP, 13083-100 ,","place":["Brazil"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0809-0250","authenticated-orcid":false,"given":"Samuel C","family":"de Assis","sequence":"additional","affiliation":[{"name":"Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM) , Rua Giuseppe M\u00e1ximo Scolfaro, 10000, Polo II de Alta Tecnologia, Campinas, SP, 13083-100 ,","place":["Brazil"]},{"name":"Faculty of Pharmaceutical Sciences, University of Campinas (UNICAMP) , Rua Candido Portinari, 200, Cidade Universit\u00e1ria Zeferino Vaz, Campinas, SP, 13083-871 ,","place":["Brazil"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6800-4425","authenticated-orcid":false,"given":"Jo\u00e3o V S","family":"Guerra","sequence":"additional","affiliation":[{"name":"Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM) , Rua Giuseppe M\u00e1ximo Scolfaro, 10000, Polo II de Alta Tecnologia, Campinas, SP, 13083-100 ,","place":["Brazil"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8471-207X","authenticated-orcid":false,"given":"Helder V","family":"Ribeiro-Filho","sequence":"additional","affiliation":[{"name":"Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM) , Rua Giuseppe M\u00e1ximo Scolfaro, 10000, Polo II de Alta Tecnologia, Campinas, SP, 13083-100 ,","place":["Brazil"]},{"name":"Faculty of Pharmaceutical Sciences, University of Campinas (UNICAMP) , Rua Candido Portinari, 200, Cidade Universit\u00e1ria Zeferino Vaz, Campinas, SP, 13083-871 ,","place":["Brazil"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,10,8]]},"reference":[{"key":"2026100808251933100_ref1","doi-asserted-by":"publisher","first-page":"169","DOI":"10.1146\/annurev-immunol-032414-112334","article-title":"T cell antigen receptor recognition of antigen-presenting molecules","volume":"33","author":"Rossjohn","year":"2015","journal-title":"Annu Rev 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