Retracted: Prediction of posttranslational modification sites from sequences with kernel methods

Abstract

Abstract:Posttranslational modification (PTM) is the chemical modification of a protein after its translation and one of the later steps in protein biosynthesis for many proteins. It plays an important role in modifying the end product of gene expression and contributes toward biological processes and diseased conditions. However, the experimental methods for identifying PTM sites are not only costly but also time consuming. Hence, computational methods are highly desired. In this article, a novel encoding method PSDP (position-specific dipeptide propensity), which is a modified version of position-specific amino acid propensity, is developed. Then, a support vector machine SVM with the kernel matrix computed by PSDP is applied to predict the PTM sites related to serine (S) and threonine (T) residues. The numerical results indicate that the performance of new method is better than the existing methods. Therefore, the new method is a useful computational resource for the identification of PTM sites. As the application, a software PTMPred is developed for predicting phosphorylation and O-glycosylation sites, and available at http://www.aporc.org/doc/wiki/PTMPred.