Fig. 4.

The process of construction of GPS 2.0 software. The training data were taken from the Phospho.ELM 6.0 database. All sites with kinase information were retained. Then these verified sites with their kinases were separated into a hierarchical structure with four levels, including group, family, subfamily, and single PK. The modified version of Group-based Phosphorylation Scoring algorithm was used. The matrix mutation was used to improve the robustness of the prediction system. Then we set the high, medium, and low thresholds based on the calculated FPR for each PK cluster. Finally GPS 2.0 was implemented in Java as the first stand alone software for computational phosphorylation.