Prediction of Peptides Binding to Major Histocompatibility Class II Molecules Using Machine Learning Methods

In daily life,we are frequently attacked by infection organisms such as bacteria and viruses. Major Histocompatibility (MHC) molecules have an essential role in T-cell activation and initiating an adaptive immune response. Development of methods for prediction of MHC-Peptide binding is important in vaccine design and immunotherapy. In this study, we try to predict the binding between peptides and MHC class II. Support vector machine (SVM) and Multi-Layer Percep-tron (MLP) are used for classification. These classifiers based on pseudo amino acid compositions of data that we ex-tracted from PseAAC server, classify the data. Since, the dataset, used in this work, is imbalanced, we apply a pre-processing step to over-sample the minority class and come over this problem. The results show that using the concept of pseudo amino acid composition and applying over-sampling method, increases the performance of predictor. Fur-thermore, the results demonstrate that using the concept of PseAAC and SVM is a successful method for the prediction of MHC class II molecules.