{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,14]],"date-time":"2026-07-14T16:28:57Z","timestamp":1784046537209,"version":"3.55.0"},"reference-count":165,"publisher":"Oxford University Press (OUP)","issue":"6","funder":[{"DOI":"10.13039\/501100006407","name":"Natural Science Foundation of Henan","doi-asserted-by":"crossref","award":["232300421156"],"award-info":[{"award-number":["232300421156"]}],"id":[{"id":"10.13039\/501100006407","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100020771","name":"Young Scientists Fund of the National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["3210151198"],"award-info":[{"award-number":["3210151198"]}],"id":[{"id":"10.13039\/501100020771","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32170677"],"award-info":[{"award-number":["32170677"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,9,23]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>As a main subtype of post-translational modification (PTM), protein lysine acylations (PLAs) play crucial roles in regulating diverse functions of proteins. With recent advancements in proteomics technology, the identification of PTM is becoming a data-rich field. A large amount of experimentally verified data is urgently required to be translated into valuable biological insights. With computational approaches, PLA can be accurately detected across the whole proteome, even for organisms with small-scale datasets. Herein, a comprehensive summary of 166 in silico PLA prediction methods is presented, including a single type of PLA site and multiple types of PLA sites. This recapitulation covers important aspects that are critical for the development of a robust predictor, including data collection and preparation, sample selection, feature representation, classification algorithm design, model evaluation, and method availability. Notably, we discuss the application of protein language models and transfer learning to solve the small-sample learning issue. We also highlight the prediction methods developed for functionally relevant PLA sites and species\/substrate\/cell-type-specific PLA sites. In conclusion, this systematic review could potentially facilitate the development of novel PLA predictors and offer useful insights to researchers from various disciplines.<\/jats:p>","DOI":"10.1093\/bib\/bbae469","type":"journal-article","created":{"date-parts":[[2024,9,24]],"date-time":"2024-09-24T21:00:08Z","timestamp":1727211608000},"source":"Crossref","is-referenced-by-count":10,"title":["Current computational tools for protein lysine acylation site prediction"],"prefix":"10.1093","volume":"25","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8490-5971","authenticated-orcid":false,"given":"Zhaohui","family":"Qin","sequence":"first","affiliation":[{"name":"Collaborative Innovation Center of Henan Grain Crops , Henan Key Laboratory of Rice Molecular Breeding and High Efficiency Production, College of Agronomy, , Zhengzhou 450046 ,","place":["China"]},{"name":"Henan Agricultural University , Henan Key Laboratory of Rice Molecular Breeding and High Efficiency Production, College of Agronomy, , Zhengzhou 450046 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haoran","family":"Ren","sequence":"additional","affiliation":[{"name":"Collaborative Innovation Center of Henan Grain Crops , Henan Key Laboratory of Rice Molecular Breeding and High Efficiency Production, College of Agronomy, , Zhengzhou 450046 ,","place":["China"]},{"name":"Henan Agricultural University , Henan Key Laboratory of Rice Molecular Breeding and High Efficiency Production, College of Agronomy, , Zhengzhou 450046 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pei","family":"Zhao","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences (CAAS) , Anyang 455000 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Agronomy, , Zhengzhou 450046 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chunbo","family":"Miao","sequence":"additional","affiliation":[{"name":"Collaborative Innovation Center of Henan Grain Crops , Henan Key Laboratory of Rice Molecular Breeding and High Efficiency Production, College of Agronomy, , Zhengzhou 450046 ,","place":["China"]},{"name":"Henan Agricultural University , Henan Key Laboratory of Rice Molecular Breeding and High Efficiency Production, College of Agronomy, , Zhengzhou 450046 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yanxiu","family":"Du","sequence":"additional","affiliation":[{"name":"Collaborative Innovation Center of Henan Grain Crops , Henan Key Laboratory of Rice Molecular Breeding and High Efficiency Production, College of Agronomy, , Zhengzhou 450046 ,","place":["China"]},{"name":"Henan Agricultural University , Henan Key Laboratory of Rice Molecular Breeding and High Efficiency Production, College of Agronomy, , Zhengzhou 450046 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Junzhou","family":"Li","sequence":"additional","affiliation":[{"name":"Collaborative Innovation Center of Henan Grain Crops , Henan Key Laboratory of Rice Molecular Breeding and High Efficiency Production, College of Agronomy, , Zhengzhou 450046 ,","place":["China"]},{"name":"Henan Agricultural University , Henan Key Laboratory of Rice Molecular Breeding and High Efficiency Production, College of Agronomy, , Zhengzhou 450046 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liuji","family":"Wu","sequence":"additional","affiliation":[{"name":"National Key Laboratory of Wheat and Maize Crop Science , College of Agronomy, , Zhengzhou 450046 ,","place":["China"]},{"name":"Henan Agricultural University , College of Agronomy, , Zhengzhou 450046 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