SAGE: A Fast Computational Tool for Linear Epitope Grafting onto a Foreign Protein Scaffold

Computational design is becoming a driving force of structural vaccinology, whereby protein antigens are engineered to generate new biomolecules with optimized immunological properties. In particular, the design of new proteins that contain multiple, different epitopes can potentially provide novel highly efficient vaccine candidates. In this context, epitope grafting, which entails the transplantation of an antibody recognition motif from one protein onto a different protein scaffold (possibly containing other immunoreactive sequences) holds great promise for the realization of superantigens. Herein, we present SAGE (strategy for alignment and grafting of epitopes), an automated computational tool for the implantation of immunogenic epitopes onto a given scaffold. It is based on the comparison between the expected secondary structures of the candidates to be grafted with all the secondary structures in the target scaffold. Evaluating the differences both in sequence and in structure between the epitope a...