OptiTope--a web server for the selection of an optimal set of peptides for epitope-based vaccines

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Abstract
Epitope-based vaccines (EVs) have recently been attracting significant interest. They trigger an immune response by confronting the immune system with immunogenic peptides derived from, e.g. viral- or cancer-related proteins. Binding of these peptides to proteins from the major histocompatibility complex (MHC) is crucial for immune system activation. However, since the MHC is highly polymorphic, different patients typically bind different repertoires of peptides. Furthermore, economical and regulatory issues impose strong limitations on the number of peptides that can be included in an EV. Hence, it is crucial to identify the optimal set of peptides for a vaccine, given constraints such as MHC allele probabilities in the target population, peptide mutation rates and maximum number of selected peptides. OptiTope aims at assisting immunologists in this critical task. With OptiTope, we provide an easy-to-use tool to determine a provably optimal set of epitopes with respect to overall immunogenicity in a specific individual (personalized medicine) or a target population (e.g. a certain ethnic group). OptiTope is available at http://www.epitoolkit.org/optitope.