PhosphoRice: a meta-predictor of rice-specific phosphorylation sites

In this paper, the phosphorylation site predictors, NetPhos 2.0, NetPhosK, Kinasephos, Scansite, Disphos and Predphosphos, were integrated to construct meta-predictors of rice-specific phosphorylation sites using several methods, including unweighted voting, unreduced weighted voting, reduced unweighted voting and weighted voting strategies. PhosphoRice, the meta-predictor produced by using weighted voting strategy with parameters selected by restricted grid search and conditional random search, performed the best at predicting phosphorylation sites in rice. Its Matthew's Correlation Coefficient (MCC) and Accuracy (ACC) reached to 0.474 and 73.8%, respectively. Compared to the best individual element predictor (Disphos_default), PhosphoRice archieved a significant increase in MCC of 0.071 (P < 0.01), and an increase in ACC of 4.6%.PhosphoRice is a powerful tool for predicting unidentified phosphorylation sites in rice. Compared to the existing methods, we found that our tool showed greater robustness in ACC and MCC. PhosphoRice is available to the public at http://bioinformatics.fafu.edu.cn/PhosphoRice webcite.Protein phosphorylation is the most common form of protein post-translational modification (PTM) [1-3]. Phosphorylation and dephosphorylation of proteins is a universal mechanism for regulating protein function in the eukaryote, prokaryote and archaea kingdoms. Given the importance of protein phosphorylation in regulating cellular signaling, large-scale identification of phosphorylated proteins has been carried out in yeast [4], mice [5], humans [6], Arabidopsis [7,8], rice [9-12] and Medicago [13]. As the data grow, the number and the size of the available phosphoprotein databases are increasing and are becoming more complex. The Phospho.ELM database contains validated phosphorylation sites that are mostly derived from mammals [14], Phosida contains large-scale data from Homo sapien and Bacillus subtilis [15], PhosphoSite (http://www.phosphosite.org/ webcite)