Abstract
Epitopes are the cornerstones for the development of rational vaccine design strategies. Conventionally, epitopes are used by chemical conjugation with the carrier protein. This chapter describes our computational epitope grafting methodology to identify the preferential grafting site in a carrier protein/scaffold. We have used the mota epitope as an example, as it was already experimentally validated by an independent group. In this chapter, we have provided sufficient details to enable the wet experimentalist to employ this computational methodology in their research objective. Scripts/programs are extensively described in this chapter and freely accessible through the provided link.
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