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

　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 cognateprotein kinases (PKs) is greatly helpful for further experimentaldesign. Although ~10 online predictors were developed, the PKclassification and control of false positive rate (FPR) were not well addressed. Here we adopted a well-established rule toclassify PKs into a hierarchical structure with four levels. Also, wedeveloped 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 alarge-scale prediction of >13,000 mammalian phosphorylation siteswith high performances. In addition, we also provided a proteome-wideprediction of Aurora-B specific substrates including protein-proteininteraction information. As the first stand-alone software forcomputational phosphorylation, GPS 2.0 will be an excellent tool forfurther experimental consideration and construction of phosphorylationnetworks.

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

GPS 2.0 User Interface