Post-protein translation modification of the prediction tool for phosphate sites-GPS 2.0

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-known rule to classify PKS into a hierarchical structure with four levels. Also, we developed a simple approach to estimate the theoretically maximal fprs.GPS 2.0

(Group-Based Prediction System

,Ver 1, 2.0

) Software was implemented in Java and cocould predict kinase-specific phosphorylation sites408

Human PKS in hierarchy. as an application, we have med 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:Http://gps.biocuckoo.org

GPS 2.0 user interface