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Here, we report an updated server, Group-based Prediction System (GPS) 6.0, for prediction of PK-specific phosphorylation sites (p-sites) in eukaryotes. First, we pre-trained a general model using penalized logistic regression (PLR), deep neural network (DNN), and Light Gradient Boosting Machine (LightGMB) on 490\u00a0762 non-redundant p-sites in 71\u00a0407 proteins. Then, transfer learning was conducted to obtain 577 PK-specific predictors at the group, family and single PK levels, using a well-curated data set of 30\u00a0043 known site-specific kinase-substrate relations in 7041 proteins. Together with the evolutionary information, GPS 6.0 could hierarchically predict PK-specific p-sites for 44046 PKs in 185 species. Besides the basic statistics, we also offered the knowledge from 22 public resources to annotate the prediction results, including the experimental evidence, physical interactions, sequence logos, and p-sites in sequences and 3D structures. The GPS 6.0 server is freely available at https:\/\/gps.biocuckoo.cn. We believe that GPS 6.0 could be a highly useful service for further analysis of phosphorylation.<\/jats:p>","DOI":"10.1093\/nar\/gkad383","type":"journal-article","created":{"date-parts":[[2023,5,10]],"date-time":"2023-05-10T19:46:03Z","timestamp":1683747963000},"page":"W243-W250","source":"Crossref","is-referenced-by-count":113,"title":["GPS 6.0: an updated server for prediction of kinase-specific phosphorylation sites in proteins"],"prefix":"10.1093","volume":"51","author":[{"given":"Miaomiao","family":"Chen","sequence":"first","affiliation":[{"name":"Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology , Wuhan 430074 , China"},{"name":"Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, College of Life Science and Technology, Huazhong University of Science and Technology , Wuhan , Hubei 430074 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Weizhi","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology , Wuhan 430074 , China"},{"name":"Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, College of Life Science and Technology, Huazhong University of Science and Technology , Wuhan , Hubei 430074 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yujie","family":"Gou","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology , Wuhan 430074 , China"},{"name":"Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, College of Life Science and Technology, Huazhong University of Science and Technology , Wuhan , Hubei 430074 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Danyang","family":"Xu","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology , Wuhan 430074 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yuxiang","family":"Wei","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology , Wuhan 430074 , China"},{"name":"Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, College of Life Science and Technology, Huazhong University of Science and Technology , Wuhan , Hubei 430074 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dan","family":"Liu","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology , Wuhan 430074 , China"},{"name":"Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, College of Life Science and Technology, Huazhong University of Science and Technology , Wuhan , Hubei 430074 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Cheng","family":"Han","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology , Wuhan 430074 , China"},{"name":"Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, College of Life Science and Technology, Huazhong University of Science and Technology , Wuhan , Hubei 430074 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xinhe","family":"Huang","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology , Wuhan 430074 , China"},{"name":"Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, College of Life Science and Technology, Huazhong University of Science and Technology , Wuhan , Hubei 430074 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chengzhi","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology , Wuhan 430074 , China"},{"name":"Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, College of Life Science and Technology, Huazhong University of Science and Technology , Wuhan , Hubei 430074 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1410-7891","authenticated-orcid":false,"given":"Wanshan","family":"Ning","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology , Wuhan 430074 , China"},{"name":"Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, College of Life Science and Technology, Huazhong University of Science and Technology , Wuhan , Hubei 430074 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Di","family":"Peng","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics and Systems 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