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Bioinformatics Tools for the Prediction of T-Cell Epitopes

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Epitope Mapping Protocols

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1785))

Abstract

T-cell responses are activated by specific peptides, called epitopes, presented on the cell surface by MHC molecules. Binding of peptides to the MHC is the most selective step in T-cell antigen presentation and therefore an essential factor in the selection of potential epitopes. Several in-vitro methods have been developed for the determination of peptide binding to MHC molecules, but these are all costly and time-consuming. In consequence, significant effort has been dedicated to the development of in-silico methods to model this event. Here, we describe two such tools, NetMHCcons and NetMHCIIpan, for the prediction of peptide binding to MHC class I and class II molecules, respectively, involved in the activation pathways of CD8+ and CD4+ T cells.

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Acknowledgments

This study was supported in part with Federal funds from the National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under Contract No. HHSN272201200010C. This work was partially funded by the Agencia Nacional de Promoción Científica y Tecnológica, Argentina (PICT-2012-0115). MN is a researcher at the Argentinean national research council (CONICET).

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Authors and Affiliations

  1. Instituto de Investigaciones Biotecnológicas, Universidad de San Martín, Buenos Aires, CP, Argentina

    Massimo Andreatta & Morten Nielsen

  2. Department of Bio and Health Informatics, Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, DK, Denmark

    Morten Nielsen

Authors
  1. Massimo Andreatta
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  2. Morten Nielsen
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Corresponding author

Correspondence to Morten Nielsen .

Editor information

Editors and Affiliations

  1. KTH School of Engineering Sciences in Chemistry, Biotechnology and Health, Protein Technology, Stockholm, Sweden

    Johan Rockberg

  2. Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada

    Johan Nilvebrant

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Andreatta, M., Nielsen, M. (2018). Bioinformatics Tools for the Prediction of T-Cell Epitopes. In: Rockberg, J., Nilvebrant, J. (eds) Epitope Mapping Protocols. Methods in Molecular Biology, vol 1785. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7841-0_18

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  • DOI: https://doi.org/10.1007/978-1-4939-7841-0_18

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7839-7

  • Online ISBN: 978-1-4939-7841-0

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