Prediction of mucin-type O-glycosylation sites by a two-staged strategy.

Molecular Diversity
Yu-Dong CaiLin Lu

Abstract

The mucin-type O-glycosylation of a protein is an important type of protein post-translational modification. This process is mediated by a family of UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferases which transfer the N-acetylgalactosamine (GalNAc) to the serine or threonine residues with unknown specificity. In order to determine the glycosylation sites of a given protein, we present a two-staged prediction method here, which first determines whether a protein is a glycoprotein, and then determines the glycosylation sites of a protein that has been predicted to be glycosylated in the first stage. In the first stage, a protein is encoded by the protein families in PFAM, which is a collective annotated database of classified protein families; then it is predicted by a predictor trained by the training set. In the second stage, nonapeptides of the predicted mucin-type glycoproteins, with serine or threonine residues at their fifth sites, are represented by indices in AAIndex. Then, it is predicted whether the nonapeptides are attached by GalNAc by a predictor, which is constructed with features selected by feature selection methods [Maximum Relevance Minimum Redundancy (mRMR) method and Incremental Feature Selection metho...Continue Reading

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Citations

Sep 21, 2013·Protein Engineering, Design & Selection : PEDS·Hua-Lin XieXi-Du Nie
Aug 7, 2012·Glycoconjugate Journal·Kun ZhouLing Yang
Oct 6, 2015·Journal of Proteomics·Elisabetta GianazzaIvano Eberini

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