EpiGASVM – a New Technique for MHC Class-II Epitope Prediction

Identification of major histocompatibility complex binding peptides is an important step in the selection of T-Cell epitope candidates suitable for usage in new vaccines.The binding groove of the MHC Class-II molecule is opened at both sides, which allows for high variability in length of the peptides that bind to this molecule and consequently complicates the prediction of the binding core motif. An accurate and efficient computational approach for the prediction of such peptides can greatly reduce the time and cost required for the design of new vaccines for infectious diseases and cancers. We have developed EpiGASVM, a new approach for the in silico prediction of MHC Class-II epitopes, by combining two artificial intelligence techniques namely: evolutionary algorithms and support vector machines. We have applied nine variations of EpiGASVM to a dataset of similarity-reduced benchmark data and we have calculated the prediction accuracy and the area under the receiver operating characteristic curve as measures of performance.The results indicate that EpiGASVM is a promising new technique that could provide researchers with a new tool for the in silico selection of candidate peptides that can be used in rational vaccine design.