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From the literature and public databases, we collected 450 378 protein lysine modification (PLM) events, and combined them with the existing data of our previously developed protein lysine modification database (PLMD 3.0). In total, CPLM 4.0 contained 592 606 experimentally identified modification events on 463 156 unique lysine residues of 105 673 proteins for up to 29 types of PLMs across 219 species. Furthermore, we carefully annotated the data using the knowledge from 102 additional resources that covered 13 aspects, including variation and mutation, disease-associated information, protein-protein interaction, protein functional annotation, DNA &amp; RNA element, protein structure, chemical-target relation, mRNA expression, protein expression\/proteomics, subcellular localization, biological pathway annotation, functional domain annotation, and physicochemical property. Compared to PLMD 3.0 and other existing resources, CPLM 4.0 achieved a &amp;gt;2-fold increase in collection of PLM events, with a data volume of \u223c45GB. We anticipate that CPLM 4.0 can serve as a more useful database for further study of PLMs.<\/jats:p>","DOI":"10.1093\/nar\/gkab849","type":"journal-article","created":{"date-parts":[[2021,9,13]],"date-time":"2021-09-13T11:12:19Z","timestamp":1631531539000},"page":"D451-D459","source":"Crossref","is-referenced-by-count":79,"title":["CPLM 4.0: an updated database with rich annotations for protein lysine modifications"],"prefix":"10.1093","volume":"50","author":[{"given":"Weizhi","family":"Zhang","sequence":"first","affiliation":[{"name":"MOE Key Laboratory of Molecular Biophysics, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaodan","family":"Tan","sequence":"additional","affiliation":[{"name":"MOE Key Laboratory of Molecular Biophysics, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shaofeng","family":"Lin","sequence":"additional","affiliation":[{"name":"MOE Key Laboratory of Molecular Biophysics, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yujie","family":"Gou","sequence":"additional","affiliation":[{"name":"MOE Key Laboratory of Molecular Biophysics, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cheng","family":"Han","sequence":"additional","affiliation":[{"name":"MOE Key Laboratory of Molecular Biophysics, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chi","family":"Zhang","sequence":"additional","affiliation":[{"name":"MOE Key Laboratory of Molecular Biophysics, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1410-7891","authenticated-orcid":false,"given":"Wanshan","family":"Ning","sequence":"additional","affiliation":[{"name":"MOE Key Laboratory of Molecular Biophysics, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chenwei","family":"Wang","sequence":"additional","affiliation":[{"name":"MOE Key Laboratory of Molecular Biophysics, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9403-6869","authenticated-orcid":false,"given":"Yu","family":"Xue","sequence":"additional","affiliation":[{"name":"MOE Key Laboratory of Molecular Biophysics, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China"},{"name":"Nanjing University Institute of Artificial Intelligence Biomedicine, Nanjing, Jiangsu 210031, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2021,9,28]]},"reference":[{"key":"2022010507313295700_B1","doi-asserted-by":"crossref","first-page":"258","DOI":"10.1038\/nrm3931","article-title":"50 years of protein acetylation: from gene regulation to epigenetics, metabolism and beyond","volume":"16","author":"Verdin","year":"2015","journal-title":"Nat. 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