NetCleave: An Open-Source Algorithm for Predicting C-Terminal Antigen Processing for MHC-I and MHC-II.

Autor:	Farriol-Duran R; Barcelona Supercomputing Center (BSC), Barcelona, Spain., Vallejo-Vallés M; Barcelona Supercomputing Center (BSC), Barcelona, Spain., Amengual-Rigo P; Barcelona Supercomputing Center (BSC), Barcelona, Spain., Floor M; Barcelona Supercomputing Center (BSC), Barcelona, Spain., Guallar V; Barcelona Supercomputing Center (BSC), Barcelona, Spain. victor.guallar@bsc.es.; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain. victor.guallar@bsc.es.
Jazyk:	angličtina
Zdroj:	Methods in molecular biology (Clifton, N.J.) [Methods Mol Biol] 2023; Vol. 2673, pp. 211-226.
DOI:	10.1007/978-1-0716-3239-0_15
Abstrakt:	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. (© 2023. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)
Databáze:	MEDLINE
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