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，蛋白质磷酸化被多种蛋白质激酶（PK）特异性催化，忠实地协调了各种生物过程，并可逆地决定了细胞动力学和可塑性。在这里，我们报告基于组的预测系统（GPS）5.0的更新算法，以提高预测激酶特定磷酸化位点（p位）的性能。开发了两种新方法：位置权重确定（PWD）和得分矩阵优化（SMO）。与其他现有工具相比，GPS 5.0具有极高的竞争力。除了丝氨酸/苏氨酸或酪氨酸激酶外，GPS 5.0还支持双特异性激酶的预测特定的p网站。在GPS 5.0的经典模块中，构建了617个单独的预测变量，用于预测479个人PK的p位。为了扩展GPS 5.0的应用，实施了一个物种特异性模块来预测161个真核生物中44,795个PK的激酶特异性p位。GPS 5.0的在线服务和本地软件包可从http://gps.biocuckoo.cn免费进行学术研究。