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However, the design of such vaccines is hindered by the possibility of weak binding affinity between the peptides and the patient\u2019s specific human leukocyte antigen (HLA) alleles, which may not elicit a robust adaptive immune response. Triggering cross-immunity by utilizing peptide mutations that have enhanced binding affinity to target HLA molecules, while preserving their homology with the original one, can be a promising avenue for neoantigen vaccine design. In this study, we introduced UltraMutate, a novel algorithm that combines Reinforcement Learning and Monte Carlo Tree Search, which identifies peptide mutations that not only exhibit enhanced binding affinities to target HLA molecules but also retains a high degree of homology with the original neoantigen. UltraMutate outperformed existing state-of-the-art methods in identifying affinity-enhancing mutations in an independent test set consisting of 3660 peptide\u2013HLA pairs. UltraMutate further showed its applicability in the design of peptide vaccines for Human Papillomavirus and Human Cytomegalovirus, demonstrating its potential as a promising tool in the advancement of personalized immunotherapy.<\/jats:p>","DOI":"10.1093\/bib\/bbae247","type":"journal-article","created":{"date-parts":[[2024,5,21]],"date-time":"2024-05-21T09:18:19Z","timestamp":1716283099000},"source":"Crossref","is-referenced-by-count":3,"title":["Integrating Reinforcement Learning and Monte Carlo Tree Search for enhanced neoantigen vaccine design"],"prefix":"10.1093","volume":"25","author":[{"given":"Yicheng","family":"Lin","sequence":"first","affiliation":[{"name":"MOE Key Laboratory of Metabolism and Molecular Medicine , Department of Biochemistry and Molecular Biology, , 131 DongAn Road, Shanghai, 200032 , China"},{"name":"School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Fudan University , Department of Biochemistry and Molecular Biology, , 131 DongAn Road, Shanghai, 200032 , China"},{"name":"State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University , 131 DongAn Road, Shanghai, 200032 , China"}]},{"given":"Jiakang","family":"Ma","sequence":"additional","affiliation":[{"name":"MOE Key Laboratory of Metabolism and Molecular Medicine , Department of Biochemistry and Molecular Biology, , 131 DongAn Road, Shanghai, 200032 , China"},{"name":"School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Fudan University , Department of Biochemistry and Molecular Biology, , 131 DongAn Road, Shanghai, 200032 , China"},{"name":"State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University , 131 DongAn Road, Shanghai, 200032 , China"}]},{"given":"Haozhe","family":"Yuan","sequence":"additional","affiliation":[{"name":"MOE Key Laboratory of Metabolism and Molecular Medicine , Department of Biochemistry and Molecular Biology, , 131 DongAn Road, Shanghai, 200032 , China"},{"name":"School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Fudan University , Department of Biochemistry and Molecular Biology, , 131 DongAn Road, Shanghai, 200032 , China"},{"name":"State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University , 131 DongAn Road, Shanghai, 200032 , China"}]},{"given":"Ziqiang","family":"Chen","sequence":"additional","affiliation":[{"name":"MOE Key Laboratory of Metabolism and Molecular Medicine , Department of Biochemistry and Molecular Biology, , 131 DongAn Road, Shanghai, 200032 , China"},{"name":"School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Fudan University , Department of Biochemistry and Molecular Biology, , 131 DongAn Road, Shanghai, 200032 , China"},{"name":"State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University , 131 DongAn Road, Shanghai, 200032 , China"}]},{"given":"Xingyu","family":"Xu","sequence":"additional","affiliation":[{"name":"MOE Key Laboratory of Metabolism and Molecular Medicine , Department of Biochemistry and Molecular Biology, , 131 DongAn Road, Shanghai, 200032 , China"},{"name":"School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Fudan University , Department of Biochemistry and Molecular Biology, , 131 DongAn Road, Shanghai, 200032 , China"},{"name":"State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University , 131 DongAn Road, Shanghai, 200032 , China"}]},{"given":"Mengping","family":"Jiang","sequence":"additional","affiliation":[{"name":"MOE Key Laboratory of Metabolism and Molecular Medicine , Department of Biochemistry and Molecular Biology, , 131 DongAn Road, Shanghai, 200032 , China"},{"name":"School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Fudan University , Department of Biochemistry and Molecular Biology, , 131 DongAn Road, Shanghai, 200032 , China"},{"name":"State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University , 131 DongAn Road, Shanghai, 200032 , China"}]},{"given":"Jialiang","family":"Zhu","sequence":"additional","affiliation":[{"name":"MOE Key Laboratory of Metabolism and Molecular Medicine , Department of Biochemistry and Molecular Biology, , 131 DongAn Road, Shanghai, 200032 , China"},{"name":"School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Fudan University , Department of Biochemistry and Molecular Biology, , 131 DongAn Road, Shanghai, 200032 , China"},{"name":"State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University , 131 DongAn Road, Shanghai, 200032 , China"}]},{"given":"Weida","family":"Meng","sequence":"additional","affiliation":[{"name":"MOE Key Laboratory of Metabolism and Molecular Medicine , Department of Biochemistry and Molecular Biology, , 131 DongAn Road, Shanghai, 200032 , China"},{"name":"School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Fudan University , Department of Biochemistry and Molecular Biology, , 131 DongAn Road, Shanghai, 200032 , China"},{"name":"State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University , 131 DongAn Road, Shanghai, 200032 , China"}]},{"given":"Wenqing","family":"Qiu","sequence":"additional","affiliation":[{"name":"Shanghai Xuhui Central Hospital , 366 North Longchuan Road, Shanghai, 200231 , China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5753-1265","authenticated-orcid":false,"given":"Yun","family":"Liu","sequence":"additional","affiliation":[{"name":"MOE Key Laboratory of Metabolism and Molecular Medicine , Department of Biochemistry and Molecular Biology, , 131 DongAn Road, Shanghai, 200032 , China"},{"name":"School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Fudan University , Department of Biochemistry and Molecular Biology, , 131 DongAn Road, Shanghai, 200032 , China"},{"name":"State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University , 131 DongAn Road, Shanghai, 200032 , China"}]}],"member":"286","published-online":{"date-parts":[[2024,5,20]]},"reference":[{"key":"2024052108570249000_ref1","doi-asserted-by":"crossref","first-page":"301","DOI":"10.1146\/annurev-genom-091212-153455","article-title":"Major histocompatibility complex genomics and human disease","volume":"14","author":"Trowsdale","year":"2013","journal-title":"Annu Rev Genomics Hum 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