Identification of peptides binding to Major Histocompatibility Complex (MHC) molecules is important for accelerating vaccine development and improving immunotherapy. Accordingly, a wide variety of prediction methods have been applied in this context. In this paper, we introduce (tree-based) ensemble classifiers for such problems and contrast their predictive performance with forefront existing methods for both MHC class I and class II molecules. In addition, we investigate the impact of differing peptide representation schemes on performance. Finally, classifier predictions are used to conduct genomewide scans of a diverse collection of HIV-1 strains, enabling assessment of epitope conservation. We investigated all combinations of six classification methods (classification trees, artificial neural networks, support vector machines, as well as the more recently devised ensemble methods (bagging, random forests, boosting) with four peptide representation schemes (amino acid sequence, select biophysical properties, select quantitative structure-activity relationship (QSAR) descriptors, and the combination of the latter two) in predicting peptide binding to an MHC class I molecule (HLA-A2) and MHC class II molecule (HLA-DR4). Our results show that the ensemble methods are consistently more accurate than the other three alternatives. Furthermore, they are robust with respect to parameter tuning. Among the four representation schemes, the amino acid sequence representation gave consistently (across classifiers) best results. This finding obviates the need for feature selection strategies incurred by use of biophysical and/or QSAR properties. We obtained, and aligned, a diverse set of 32 HIV-1 genomes and pursued genomewide HLA-DR4 epitope profiling by querying with respect to classifier predictions, as obtained under each of the four peptide representation schemes. We validated those epitopes conserved across strains against known T-cell epitopes. Once again, amino acid sequence representation was at least as effective as using properties. Assessment of novel epitope predictions awaits experimental verification.
