A new machine learning approach for protein phosphorylation site prediction in plants

Abstract

Protein phosphorylation is a crucial regulatory mechanism in various organisms. With recent improvements in mass spectrometry, phosphorylationsite data are rapidly accumulating. Despite this wealth of data, computational prediction of phosphorylation sites remains a challenging task. This is particularly true in plants, due to the limited information on substrate specificities of protein kinases in plants and the fact that current phosphorylation prediction tools are trained with kinase-specific phosphorylation data from non-plant organisms. In this paper, we proposed a new machine learning approach for phosphorylation site prediction. We incorporate protein sequence information and protein disordered regions, and integrate machine learning techniques of knearest neighbor and support vector machine for redicting phosphorylation sites. Test results on the PhosPhAt dataset of phosphoserines in Arabidopsis and the TAIR7 non-redundant protein database show good performance of our proposed phosphorylation site prediction method. © Springer-Verlag Berlin Heidelberg 2009.