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Experimental validation such peptides is extremely resource-intensive. As a result, accurate computational prediction of binding peptides is highly important, particularly in the context of cancer immunotherapy applications, such as the identification of neoantigens. In recent years, there is a significant need to continually improve the existing prediction methods to meet the demands of this field. We developed ConvNeXt-MHC, a method for predicting MHC-I-peptide binding affinity. It introduces a degenerate encoding approach to enhance well-established panspecific methods and integrates transfer learning and semi-supervised learning methods into the cutting-edge deep learning framework ConvNeXt. Comprehensive benchmark results demonstrate that ConvNeXt-MHC outperforms state-of-the-art methods in terms of accuracy. We expect that ConvNeXt-MHC will help us foster new discoveries in the field of immunoinformatics in the distant future. We constructed a user-friendly website at http:\/\/www.combio-lezhang.online\/predict\/, where users can access our data and application.<\/jats:p>","DOI":"10.1093\/bib\/bbae133","type":"journal-article","created":{"date-parts":[[2024,4,2]],"date-time":"2024-04-02T04:50:57Z","timestamp":1712033457000},"source":"Crossref","is-referenced-by-count":16,"title":["ConvNeXt-MHC: improving MHC\u2013peptide affinity prediction by structure-derived degenerate coding and the ConvNeXt model"],"prefix":"10.1093","volume":"25","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3708-1727","authenticated-orcid":false,"given":"Le","family":"Zhang","sequence":"first","affiliation":[{"name":"College of Computer Science, Sichuan University , Chengdu 610065 , China"}]},{"given":"Wenkai","family":"Song","sequence":"additional","affiliation":[{"name":"College of Computer Science, Sichuan University , Chengdu 610065 , China"}]},{"given":"Tinghao","family":"Zhu","sequence":"additional","affiliation":[{"name":"College of Computer Science, Sichuan University , Chengdu 610065 , China"},{"name":"Nuclear Power Institute of China , Chengdu 610213 , China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2517-9436","authenticated-orcid":false,"given":"Yang","family":"Liu","sequence":"additional","affiliation":[{"name":"Center of Growth , Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, , No. 29 Wangjiang Road, Chengdu 610065 , China"},{"name":"Sichuan University , Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, , No. 29 Wangjiang Road, Chengdu 610065 , China"}]},{"given":"Wei","family":"Chen","sequence":"additional","affiliation":[{"name":"Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine , Chengdu 611137 , China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1925-2123","authenticated-orcid":false,"given":"Yang","family":"Cao","sequence":"additional","affiliation":[{"name":"Center of Growth , Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, , No. 29 Wangjiang Road, Chengdu 610065 , China"},{"name":"Sichuan University , Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, , No. 29 Wangjiang Road, Chengdu 610065 , China"}]}],"member":"286","published-online":{"date-parts":[[2024,4,1]]},"reference":[{"key":"2024040204504653500_ref1","article-title":"Major histocompatibility complex: interaction with peptides. 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