Bioinformatic Techniques for Vaccine Development: Epitope Prediction and Structural Vaccinology

Structural vaccinology involves characterizing the interactions between an antigen and antibodies or host immune receptors. Central to this is the task of epitope prediction, which involves describing the binding affinity and interactions of a given peptide typically to the major histocompatibility complex in the case of T-cells or to the antibodies in the case of B-cells. Several computational models exist for this purpose which we will review here. Generally, epitope predictions for MHC-I and MHC-II are substantially different tasks as well as epitope prediction for continuous versus discontinuous B-cell epitopes. Overall, these models suffer from overprediction of epitopes although general themes support both the use of neural networks as well as the incorporation of more abundant and more varied experimental annotation into model training as valuable in improving predictive performance.