(1)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 430074, China.
(1)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 430074, China; (2)Huazhong University of Science and Technology Ezhou Industrial Technology Research Institute, Ezhou 436044, China.
Genomics Proteomics Bioinformatics. 2020 Feb;18(1):72-80. doi: 10.1016/j.gpb.2020.01.001. Epub 2020 Mar 19.
In eukaryotes, protein phosphorylation is specifically catalyzed by numerous protein kinases (PKs), faithfully orchestrates various biological processes, and reversibly determines cellular dynamics and plasticity. Here we report an updated algorithm of Group-based Prediction System (GPS) 5.0 to improve the performance for predicting kinase-specific phosphorylation sites (p-sites). Two novel methods, position weight determination (PWD) and scoring matrix optimization (SMO), were developed. Compared with other existing tools, GPS 5.0 exhibits a highly competitive accuracy. Besides serine/threonine or tyrosine kinases, GPS 5.0 also supports the prediction of dual-specificity kinase-specific p-sites. In the classical module of GPS 5.0, 617 individual predictors were constructed for predicting p-sites of 479 human PKs. To extend the application of GPS 5.0, a species-specific module was implemented to predict kinase-specific p-sites for 44,795 PKs in 161 eukaryotes. The online service and local packages of GPS 5.0 are freely available for academic research at http://gps.biocuckoo.cn.
在真核生物中，蛋白质磷酸化是由众多蛋白激酶（PKs）特异性催化的，它精确地调控着各种生物过程，并能可逆地决定细胞的动态和可塑性。在这里，我们报告了 Group-based Prediction System（GPS）5.0 的一个更新算法，用于提高预测激酶特异性磷酸化位点（p-sites）的性能。我们开发了两种新方法，即位置权重确定（PWD）和评分矩阵优化（SMO）。与其他现有的工具相比，GPS 5.0 表现出了高度竞争的准确性。除了丝氨酸/苏氨酸或酪氨酸激酶之外，GPS 5.0 还支持双特异性激酶特异性 p-sites 的预测。在 GPS 5.0 的经典模块中，我们构建了 617 个个体预测器，用于预测 479 个人类 PKs 的 p-sites。为了扩展 GPS 5.0 的应用范围，我们实现了一个物种特异性模块，用于预测 161 种真核生物中的 44795 个 PKs 的激酶特异性 p-sites。GPS 5.0 的在线服务和本地包可免费用于学术研究，网址是 http://gps.biocuckoo.cn。
