Abstract
T cell epitopes presented on the surface of mammalian cells are subjected to a complex network of antigen processing and presentation. Among them, C-terminal antigen processing constitutes one of the main bottlenecks for the generation of epitopes, as it defines the C-terminal end of the final epitope and delimits the peptidome that will be presented downstream. Previously (Amengual-Rigo and Guallar, Sci Rep 111(11):1–8, 2021), we demonstrated that NetCleave stands out as one of the best algorithms for the prediction of C-terminal processing, which in its turn can be crucial to design peptide-based vaccination strategies. In this chapter, we provide a pipeline to exploit the full capabilities of NetCleave, an open-source and retrainable algorithm for predicting the C-terminal antigen processing for the MHC-I and MHC-II pathways.
Roc Farriol-Duran and Marina Vallejo-Vallés are co-first authors.
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Farriol-Duran, R., Vallejo-Vallés, M., Amengual-Rigo, P., Floor, M., Guallar, V. (2023). NetCleave: An Open-Source Algorithm for Predicting C-Terminal Antigen Processing for MHC-I and MHC-II. In: Reche, P.A. (eds) Computational Vaccine Design. Methods in Molecular Biology, vol 2673. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3239-0_15
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DOI: https://doi.org/10.1007/978-1-0716-3239-0_15
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