※ GPS INTRODUCTION:
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 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.
Recently, we released GPS 3.0 (Group-based Prediction System, ver 3.0) with a novel Motif length selection and Weight training method to improve the prediction performance and robustness greatly. In addition, GPS 3.0 could predict predict kinase-specific phosphorylation sites for 464 human PKs in hierarchy.
The GPS 3.0 is freely available at: http://gps.biocuckoo.org
This website is linked in ExPASy Proteomics Tools page.
GPS 3.0 User Interface
For publication of results please cite the following article:
GPS 3.0: Hierarchical prediction of kinase-specific phosphorylation sites
Yongbo Wang, Han Cheng, Zexian Liu, Wankun Deng, Zhicheng Pan and Yu Xue*.
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