{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,19]],"date-time":"2026-08-19T05:25:23Z","timestamp":1787117123395,"version":"build-2736575974"},"reference-count":0,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2026,8,19]],"date-time":"2026-08-19T00:00:00Z","timestamp":1787097600000},"content-version":"am","delay-in-days":1,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Post-translational modifications (PTMs) are pivotal in modulating protein function and cellular processes. However, experimental identification of PTM sites remains costly and labor-intensive. Recent advances in artificial intelligence (AI) have enabled accurate and scalable in silico PTM site prediction from large-scale proteomic data. In this review, we provide a comprehensive and up-to-date overview of AI-driven PTM site prediction across more than ten PTM classes, covering single-PTM site prediction, multiple-PTM site prediction, inter-site crosstalk prediction, and functional prediction of modification sites. We systematically analyze and compare key AI frameworks, from conventional machine learning to deep learning, and summarize representative tools. We also identify key challenges and propose future directions for improvement. To facilitate application and ongoing progress, we provide practical guidelines for method selection and have established a dedicated website, which serves as a community benchmarking resource for the development of PTM site prediction tools. This website will be regularly updated with emerging prediction tools. By integrating comprehensive literature analysis with a dynamic online resource, we aim to provide a reliable foundation for understanding current capabilities and guiding the future development of PTM site prediction tools, thereby promoting the integration of AI into practical biomedical research applications.<\/jats:p>","DOI":"10.1093\/gpbjnl\/qzag088","type":"journal-article","created":{"date-parts":[[2026,8,19]],"date-time":"2026-08-19T04:40:17Z","timestamp":1787114417000},"source":"Crossref","is-referenced-by-count":0,"title":["Artificial Intelligence in Post-translational Modification Site Prediction: Progress and Future Perspectives"],"prefix":"10.1093","author":[{"given":"Jiayi","family":"Ran","sequence":"first","affiliation":[{"name":"Zhejiang University Department of Respiratory and Critical Care Medicine, the Second Affiliated Hospital, and Centre for Infection Immunity and Cancer of Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, , Hangzhou 310029,","place":["China"]},{"name":"The University of Edinburgh Edinburgh Medical School: Biomedical Sciences, College of Medicine and Veterinary Medicine, , Edinburgh EH16 4SB,","place":["UK"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaohan","family":"Zhang","sequence":"additional","affiliation":[{"name":"Zhejiang University Department of Respiratory and Critical Care Medicine, the Second Affiliated Hospital, and Centre for Infection Immunity and Cancer of Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, , Hangzhou 310029,","place":["China"]},{"name":"The University of Edinburgh Edinburgh Medical School: Biomedical Sciences, College of Medicine and Veterinary Medicine, , Edinburgh EH16 4SB,","place":["UK"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yunze","family":"Wang","sequence":"additional","affiliation":[{"name":"Zhejiang University Department of Respiratory and Critical Care Medicine, the Second Affiliated Hospital, and Centre for Infection Immunity and Cancer of Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, , Hangzhou 310029,","place":["China"]},{"name":"The University of Edinburgh Edinburgh Medical School: Biomedical Sciences, College of Medicine and Veterinary Medicine, , Edinburgh EH16 4SB,","place":["UK"]},{"name":"Zhejiang University Zhejiang University-University of Edinburgh Institute Cross Lung Research Alliance, International Joint Center for Biomedical Sciences, , Haining 314400, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Silin","family":"Chen","sequence":"additional","affiliation":[{"name":"Zhejiang University Department of Respiratory and Critical Care Medicine, the Second Affiliated Hospital, and Centre for Infection Immunity and Cancer of Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, , Hangzhou 310029,","place":["China"]},{"name":"The University of Edinburgh Edinburgh Medical School: Biomedical Sciences, College of Medicine and Veterinary Medicine, , Edinburgh EH16 4SB,","place":["UK"]},{"name":"Zhejiang University Zhejiang University-University of Edinburgh Institute Cross Lung Research Alliance, International Joint Center for Biomedical Sciences, , Haining 314400, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiaqi","family":"Deng","sequence":"additional","affiliation":[{"name":"Zhejiang University Department of Respiratory and Critical Care Medicine, the Second Affiliated Hospital, and Centre for Infection Immunity and Cancer of Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, , Hangzhou 310029,","place":["China"]},{"name":"The University of Edinburgh Edinburgh Medical School: Biomedical Sciences, College of Medicine and Veterinary Medicine, , Edinburgh EH16 4SB,","place":["UK"]},{"name":"Zhejiang University Zhejiang University-University of Edinburgh Institute Cross Lung Research Alliance, International Joint Center for Biomedical Sciences, , Haining 314400, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Martin","family":"Kosar","sequence":"additional","affiliation":[{"name":"Zhejiang University-University of Edinburgh Institute , , Haining 314400,","place":["China"]},{"name":"Zhejiang University School of Medicine , , Haining 314400,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bo","family":"Yang","sequence":"additional","affiliation":[{"name":"Zhejiang University Department of Respiratory and Critical Care Medicine, the Second Affiliated Hospital, and Centre for Infection Immunity and Cancer of Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, , Hangzhou 310029,","place":["China"]},{"name":"The University of Edinburgh Edinburgh Medical School: Biomedical Sciences, College of Medicine and Veterinary Medicine, , Edinburgh EH16 4SB,","place":["UK"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Huiran","family":"Wang","sequence":"additional","affiliation":[{"name":"Zhejiang University Department of Respiratory and Critical Care Medicine, the Second Affiliated Hospital, and Centre for Infection Immunity and Cancer of Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, , Hangzhou 310029,","place":["China"]},{"name":"The University of Edinburgh Edinburgh Medical School: Biomedical Sciences, College of Medicine and Veterinary Medicine, , Edinburgh EH16 4SB,","place":["UK"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yishu","family":"Deng","sequence":"additional","affiliation":[{"name":"Zhejiang University Department of Respiratory and Critical Care Medicine, the Second Affiliated Hospital, and Centre for Infection Immunity and Cancer of Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, , Hangzhou 310029,","place":["China"]},{"name":"The University of Edinburgh Edinburgh Medical School: Biomedical Sciences, College of Medicine and Veterinary Medicine, , Edinburgh EH16 4SB,","place":["UK"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tailin","family":"Li","sequence":"additional","affiliation":[{"name":"Zhejiang University Department of Respiratory and Critical Care Medicine, the Second Affiliated Hospital, and Centre for Infection Immunity and Cancer of Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, , Hangzhou 310029,","place":["China"]},{"name":"The University of Edinburgh Edinburgh Medical School: Biomedical Sciences, College of Medicine and Veterinary Medicine, , Edinburgh EH16 4SB,","place":["UK"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yufei","family":"Liu","sequence":"additional","affiliation":[{"name":"Zhejiang University Department of Respiratory and Critical Care Medicine, the Second Affiliated Hospital, and Centre for Infection Immunity and Cancer of Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, , Hangzhou 310029,","place":["China"]},{"name":"The University of Edinburgh Edinburgh Medical School: Biomedical Sciences, College of Medicine and Veterinary Medicine, , Edinburgh EH16 4SB,","place":["UK"]},{"name":"Zhejiang University Zhejiang University-University of Edinburgh Institute Cross Lung Research Alliance, International Joint Center for Biomedical Sciences, , Haining 314400, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lian","family":"Wang","sequence":"additional","affiliation":[{"name":"Zhejiang University Department of Thoracic Surgery, the Second Affiliated Hospital, Zhejiang University School of Medicine, , Hangzhou 310009,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yijiang","family":"Guo","sequence":"additional","affiliation":[{"name":"Zhejiang University Department of Respiratory and Critical Care Medicine, the Second Affiliated Hospital, and Centre for Infection Immunity and Cancer of Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, , Hangzhou 310029,","place":["China"]},{"name":"The University of Edinburgh Edinburgh Medical School: Biomedical Sciences, College of Medicine and Veterinary Medicine, , Edinburgh EH16 4SB,","place":["UK"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaochen","family":"Zhang","sequence":"additional","affiliation":[{"name":"Zhejiang University School of Medicine Department of Medical Oncology, The First Affiliated Hospital, , Hangzhou 310003,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Huaqiong","family":"Huang","sequence":"additional","affiliation":[{"name":"Second Affiliated Hospital of Zhejiang University School of Medicine Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care Medicine, , Hangzhou 310009,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jianya","family":"Zhou","sequence":"additional","affiliation":[{"name":"The First Affiliated Hospital Department of Respiratory Disease, Thoracic Disease Center, , College of Medicine, , Hangzhou 310003,","place":["China"]},{"name":"Zhejiang University Department of Respiratory Disease, Thoracic Disease Center, , College of Medicine, , Hangzhou 310003,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jing","family":"Zheng","sequence":"additional","affiliation":[{"name":"The First Affiliated Hospital Department of Respiratory Disease, Thoracic Disease Center, , College of Medicine, , Hangzhou 310003,","place":["China"]},{"name":"Zhejiang University Department of Respiratory Disease, Thoracic Disease Center, , College of Medicine, , Hangzhou 310003,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhihao","family":"Xu","sequence":"additional","affiliation":[{"name":"Zhejiang University Department of Respiratory and Critical Care Medicine, the Fourth Affiliated Hospital of School of Medicine, and International School of Medicine, International Institutes of Medicine, , Yiwu 322000,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yong","family":"Tang","sequence":"additional","affiliation":[{"name":"Shenzhen Nanshan People\u2019s Hospital Department of Thoracic Surgery, , Shenzhen 518052,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jian","family":"Liu","sequence":"additional","affiliation":[{"name":"Zhejiang University Department of Respiratory and Critical Care Medicine, the Second Affiliated Hospital, and Centre for Infection Immunity and Cancer of Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, , Hangzhou 310029,","place":["China"]},{"name":"The University of Edinburgh Edinburgh Medical School: Biomedical Sciences, College of Medicine and Veterinary Medicine, , Edinburgh EH16 4SB,","place":["UK"]},{"name":"Zhejiang University Zhejiang University-University of Edinburgh Institute Cross Lung Research Alliance, International Joint Center for Biomedical Sciences, , Haining 314400, China"},{"name":"Zhejiang Key Laboratory of Medical Imaging Artificial Intelligence , Haining 314400, China"},{"name":"Zhejiang University Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, , Hangzhou 310058, China"},{"name":"Biomedical and Health Translational Research Center of Zhejiang Province , Haining 314400, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,8,18]]},"container-title":["Genomics, Proteomics &amp; 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