GPS 2.0, a Tool to Predict Kinase-specific Phosphorylation Sites in Hierarchy

最新推荐文章于 2021-10-19 16:23:47 发布

最新推荐文章于 2021-10-19 16:23:47 发布 · 356 阅读

GPS2.0是一款用于预测特定蛋白激酶磷酸化位点的软件，能够针对408种人类蛋白激酶进行层级化的预测。通过采用成熟的规则对蛋白激酶进行分类，并估算理论上最大的假阳性率，GPS2.0有助于实验设计并构建磷酸化网络。

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　GPS 2.0, a Tool to Predict Kinase-specific Phosphorylation Sites in Hierarchy
　 Yu Xue , Jian Ren , Xinjiao Gao, Changjiang Jin, Longping Wen, and Xuebiao Yao
　Mol Cell Proteomics.2008 ; 7: 1598-1608

　 [Abstract] [Full Text] [Supplemental Data]

Computational prediction of phosphorylation sites with their cognate protein kinases (PKs) is greatly helpful for further experimental design. Although ~10 online predictors were developed, the PK classification and control of false positive rate (FPR ) were not well addressed. Here we adopted a well-established rule to classify PKs into a hierarchical structure with four levels. Also, we developed a simple approach to estimate the theoretically maximal FPRs. Then GPS 2.0 (Group-based Prediction System , ver 2.0 ) software was implemented in JAVA and could predict kinase-specific phosphorylation sites for 408 human PKs in hierarchy. As an application, we performed a large-scale prediction of >13,000 mammalian phosphorylation sites with high performances. In addition, we also provided a proteome-wide prediction of Aurora-B specific substrates including protein-protein interaction information. As the first stand-alone software for computational phosphorylation, GPS 2.0 will be an excellent tool for further experimental consideration and construction of phosphorylation networks.

The GPS 2.0 is freely available at: http://gps.biocuckoo.org