Computational prediction of phosphorylation sites (p-sites) with their cognate protein kinases (PKs) is greatly helpful for further experimental design. Previously, our group developed and maintained a series of PK-specific p-site predictors. In 2005, we presented the first Group-based Phosphorylation Scoring (GPS) webserver, based on the hypothesis that similar short peptides exhibit similar biochemical properties for modification, including 71 PK-specific p-site predictors. Later, we improved GPS algorithm and developed GPS 2.0 (renamed as Group-based Prediction System) software. As the first standalone software for p-site prediction, GPS 2.0 provides 408 human PK-specific p-site predictions in hierarchy. Then, GPS 2.1 were further implemented with an optimized algorithm of motif length selection (MLS) to detect the optimal length of phosphorylation site peptide (PSP). Since its release, GPS series have been widely used and prompted many biological discoveries.

Recently, we released GPS 3.0 with novel approach of position weight determination (PWD) by merging motif length selection (MLS) and weight training (WT) to automatically detect informative positions and optimize weight parameters. More than 10,000 p-sites were used for training and GPS 3.0 achieved better performances than other existing tools. To extend the application, the PK classifications of 161 species from previously developed database iEKPD were mapped. In total, GPS 3.0 could predict potential p-sites for 521 human PKs in hierarchy, and more than 68,042 PKs for other species. In addition, structural features such as secondary structures, surface accessibilities and disorder regions were annotated for the predicted p-sites.

The GPS 3.0 is freely available at: http://gps.biocuckoo.cn

This website is linked in ExPASy Proteomics Tools page.

For publication of results please cite the following article:

2019, Submitted

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]

GPS: a comprehensive www server for phosphorylation sites prediction. Yu Xue, Fengfeng Zhou, Minjie Zhu, Kashif Ahmed, Guoliang Chen and Xuebiao Yao*. Nucleic Acids Res. 2005; 33 (suppl 2): W184-W187

[Abstract] [Full Text]

GPS 2.1: enhanced prediction of kinase-specific phosphorylation sites with an algorithm of motif length selection. Yu Xue, Zexian Liu, Jun Cao, Qian Ma, Xinjiao Gao, Qingqi Wang, Changjiang Jin, Yanhong Zhou, Longping Wen, and Jian Ren. Protein Engineering, Design and Selection (2011);24 (3): 255-260

[Abstract] [Full Text] [Supplemental Data]