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.
真核生物中，蛋白激酶通过特异性磷酸化底物蛋白质参与调控许多重要生物学过程，并可逆地决定了细胞的动力学和可塑性。本研究中，我们基于已有的算法基础，设计了新版本的分组打分系统（Group-based Prediction System, GPS）5.0算法，提出了“位置权重决定”（Position weight determination, PWD）和“打分矩阵优化”（Scoring matrix optimization, SMO）两个新方法，并利用“惩罚逻辑回归”（Penalized logistic regression, PLR）算法训练模型，显著提高了激酶特异性磷酸化位点的预测准确性。与其他工具相比，GPS 5.0具有更高的准确性。除丝氨酸/苏氨酸激酶或酪氨酸激酶外，GPS 5.0还提供了针对双特异性激酶的位点预测。GPS 5.0软件包括两个模块，其中经典模块构建了617个独立的预测器，可针对人类479个蛋白激酶进行预测；物种特异性模块可住准确预测161种真核生物中44,795个激酶的特异性位点。GPS 5.0的本地软件及在线预测工具获取可访问链接：http://gps.biocuckoo.cn。





PDF全文下载地址:

http://gpb.big.ac.cn/articles/download/766