NetCleave: an open-source algorithm for predicting C-terminal antigen processing for MHC-I and MHC-II

Abstract Antigens presented on the cell surface have been subjected to multiple biological processes. Among them, C-terminal antigen processing constitutes one of the main bottlenecks of the peptide presentation pathways, as it delimits the peptidome that will be subjected downstream. Here, we prese...

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Autores principales:	Pep Amengual-Rigo, Victor Guallar
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/e0a1516e95b44526a5d40b1147d14315
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spelling	oai:doaj.org-article:e0a1516e95b44526a5d40b1147d143152021-12-02T17:14:30ZNetCleave: an open-source algorithm for predicting C-terminal antigen processing for MHC-I and MHC-II10.1038/s41598-021-92632-y2045-2322https://doaj.org/article/e0a1516e95b44526a5d40b1147d143152021-06-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-92632-yhttps://doaj.org/toc/2045-2322Abstract Antigens presented on the cell surface have been subjected to multiple biological processes. Among them, C-terminal antigen processing constitutes one of the main bottlenecks of the peptide presentation pathways, as it delimits the peptidome that will be subjected downstream. Here, we present NetCleave, an open-source and retrainable algorithm for the prediction of the C-terminal antigen processing for both MHC-I and MHC-II pathways. NetCleave architecture consists of a neural network trained on 46 different physicochemical descriptors of the cleavage site amino acids. Our results demonstrate that prediction of C-terminal antigen processing achieves high accuracy on MHC-I (AUC of 0.91), while it remains challenging for MHC-II (AUC of 0.66). Moreover, we evaluated the performance of NetCleave and other prediction tools for the evaluation of four independent immunogenicity datasets (H2-Db, H2-Kb, HLA-A*02:01 and HLA-B:07:02). Overall, we demonstrate that NetCleave stands out as one of the best algorithms for the prediction of C-terminal processing, and we provide one of the first evidence that C-terminal processing predictions may help in the discovery of immunogenic peptides.Pep Amengual-RigoVictor GuallarNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-8 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Pep Amengual-Rigo Victor Guallar NetCleave: an open-source algorithm for predicting C-terminal antigen processing for MHC-I and MHC-II
description	Abstract Antigens presented on the cell surface have been subjected to multiple biological processes. Among them, C-terminal antigen processing constitutes one of the main bottlenecks of the peptide presentation pathways, as it delimits the peptidome that will be subjected downstream. Here, we present NetCleave, an open-source and retrainable algorithm for the prediction of the C-terminal antigen processing for both MHC-I and MHC-II pathways. NetCleave architecture consists of a neural network trained on 46 different physicochemical descriptors of the cleavage site amino acids. Our results demonstrate that prediction of C-terminal antigen processing achieves high accuracy on MHC-I (AUC of 0.91), while it remains challenging for MHC-II (AUC of 0.66). Moreover, we evaluated the performance of NetCleave and other prediction tools for the evaluation of four independent immunogenicity datasets (H2-Db, H2-Kb, HLA-A*02:01 and HLA-B:07:02). Overall, we demonstrate that NetCleave stands out as one of the best algorithms for the prediction of C-terminal processing, and we provide one of the first evidence that C-terminal processing predictions may help in the discovery of immunogenic peptides.
format	article
author	Pep Amengual-Rigo Victor Guallar
author_facet	Pep Amengual-Rigo Victor Guallar
author_sort	Pep Amengual-Rigo
title	NetCleave: an open-source algorithm for predicting C-terminal antigen processing for MHC-I and MHC-II
title_short	NetCleave: an open-source algorithm for predicting C-terminal antigen processing for MHC-I and MHC-II
title_full	NetCleave: an open-source algorithm for predicting C-terminal antigen processing for MHC-I and MHC-II
title_fullStr	NetCleave: an open-source algorithm for predicting C-terminal antigen processing for MHC-I and MHC-II
title_full_unstemmed	NetCleave: an open-source algorithm for predicting C-terminal antigen processing for MHC-I and MHC-II
title_sort	netcleave: an open-source algorithm for predicting c-terminal antigen processing for mhc-i and mhc-ii
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/e0a1516e95b44526a5d40b1147d14315
work_keys_str_mv	AT pepamengualrigo netcleaveanopensourcealgorithmforpredictingcterminalantigenprocessingformhciandmhcii AT victorguallar netcleaveanopensourcealgorithmforpredictingcterminalantigenprocessingformhciandmhcii
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NetCleave: an open-source algorithm for predicting C-terminal antigen processing for MHC-I and MHC-II

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