Prediction of MHC class I binding peptides with a new feature encoding technique

The recognition of specific peptides, bound to major histocompatibility complex (MHC) class I molecules, is of particular importance to the robust identification of T-cell epitopes and thus the successful design of protein-based vaccines. Here, we present a new feature amino acid encoding technique termed OEDICHO to predict MHC class I/peptide complexes. In the proposed method, we have combined orthonormal encoding (OE) and the binary representation of selected 10 best physicochemical properties of amino acids derived from Amino Acid Index Database (AAindex). We also have compared our method to current feature encoding techniques. The tests have been carried out on comparatively large Human Leukocyte Antigen (HLA)-A and HLA-B allele peptide binding datasets. Empirical results show that our amino acid encoding scheme leads to better classification performance on a standalone classifier.