Predicting protein N-glycosylation by combining functional domain and secretion information

Protein N-glycosylation plays an important role in protein function. Yet, at present, few computational methods are available for the prediction of this protein modification. This prompted our development of a support vector machine (SVM)-based method for this task, as well as a partial least squares (PLS) regression based prediction method for comparison. A functional domain feature space was used to create SVM and PLS models, which achieved accuracies of 83.91% and 79.89%, respectively, as evaluated by a leave-one-out cross-validation. Subsequently, SVM and PLS models were developed based on functional domain and protein secretion information, which yielded accuracies of 89.13% and 86%, respectively. This analysis demonstrates that the protein functional domain and secretion information are both efficient predictors of N-glycosylation.