{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,24]],"date-time":"2025-11-24T12:14:02Z","timestamp":1763986442769,"version":"3.45.0"},"reference-count":183,"publisher":"MDPI AG","issue":"12","license":[{"start":{"date-parts":[[2025,11,24]],"date-time":"2025-11-24T00:00:00Z","timestamp":1763942400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["62502242"],"award-info":[{"award-number":["62502242"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100017700","name":"Henan Provincial Science and Technology Research Project","doi-asserted-by":"publisher","award":["252102220039"],"award-info":[{"award-number":["252102220039"]}],"id":[{"id":"10.13039\/501100017700","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Key Research Project Plan for Higher Education Institutions of Henan Province","award":["24A520027"],"award-info":[{"award-number":["24A520027"]}]},{"name":"Science and Technology Research Project of Nangyang","award":["24KJGG059"],"award-info":[{"award-number":["24KJGG059"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Information"],"abstract":"<jats:p>Post-translational modifications (PTMs) of proteins are essential for cellular function. Owing to the high cost and time demands of high-throughput sequencing, machine learning and deep learning methods are being rapidly developed for predicting PTM sites. This manuscript presents a comprehensive review of the current research on the application of intelligent algorithms for predicting PTM sites. It outlines the key steps for identifying modified sites based on intelligent algorithms, including data pre-processing, feature extraction, dimension reduction, and classifier development. This review also discusses potential future research directions in this field, providing valuable insights for advancing the state-of-the-art PTM site prediction. Collectively, this review provides comprehensive knowledge on PTM identification and contributes to the development of advanced predictors in the future.<\/jats:p>","DOI":"10.3390\/info16121023","type":"journal-article","created":{"date-parts":[[2025,11,24]],"date-time":"2025-11-24T11:47:22Z","timestamp":1763984842000},"page":"1023","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Role of Machine and Deep Learning in Predicting Protein Modification Sites: Review and Future Directions"],"prefix":"10.3390","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0009-0009-8386-5432","authenticated-orcid":false,"given":"Siliang","family":"Gong","sequence":"first","affiliation":[{"name":"School of Computer and Software, Nanyang Institute of Technology, Nanyang 473000, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6564-6601","authenticated-orcid":false,"given":"Kaiyang","family":"Qu","sequence":"additional","affiliation":[{"name":"School of Computer and Software, Nanyang Institute of Technology, Nanyang 473000, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2025,11,24]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Shrestha, P., Kandel, J., Tayara, H., and Chong, K.T. 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