Protein phosphorylation site prediction via feature discovery support vector machine

Protein phosphorylation/dephosphorylation is the central mechanism of post-translational modification which regulates cellular responses and phenotypes. Due to the efficiency and resource constraints of the in vivo methods for identifying phosphorylation sites, there is a strong motivation to computationally predict potential phosphorylation sites. In this work, we propose to use a unique set of features to represent the peptides surrounding the amino acid sites of interest and use feature selection support vector machine to predict whether the serine/threonine sites are potentially phosphorylable, as well as selecting important features that may lead to phosphorylation. Experimental results indicate that the new features and the prediction method can more effectively predict protein phosphorylation sites than the existing state of the art methods. The features selected by our prediction model provide biological insights to the in vivo phosphorylation.