Protein phosphorylation, one of the most ubiquitous post-translational modifications (PTM), is catalyzed by protein kinases (PKs). Each PK only modifies a specific set of substrates to ensure signaling fidelity, and defects of PK functions often induce a variety of diseases, including cancers1. Thus, identification of PK-specific phosphorylation sites is essential for molecular delineation of signaling cascade of physiology and potential intervention of pathology of diseases. This motivated the development of the Group-based Phosphorylation Scoring (GPS) algorithm1-3.
GPS algorithm is based on the hypothesis that the pattern of phosphorylation sites of a specific PK might be compromised by heterogeneity of multiple structural determinants with different features. In this regard, we partition the known phosphorylation sites of each PK into several groups, and predict the query peptide as the phosphorylation site if it is significantly similar in sequence to the known phosphorylation sites in at least one group. The details of the algorithm can be found in our previously published works 2, 3.
The current version 1.10 of GPS web service provides the prediction of phosphorylation sites for 71 PK groups, including 216 unique PKs, and is freely available at "http://bioinformatics.lcd-ustc.org/gps_web":http://bioinformatics.lcd-ustc.org/gps_web. The following protocol describes how to use GPS to predict the PK-specific phosphorylation sites, and to choose potentially interesting candidates for further consideration.