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Immunoinformatics pp 185–200Cite as

Prediction of Peptide-MHC Binding Using Profiles

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Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 409))

Summary

Prediction of peptide binding to major histocompatibility complex (MHC) molecules is a basis for anticipating T-cell epitopes. Peptides that bind to a given MHC molecule are related by sequence similarity. Therefore, a position-specific scoring matrix (PSSM)—also known as profile—derived from a set of aligned peptides known to bind to a given MHC molecule can be used as a predictor of both peptide–MHC binding and T-cell epitopes. In this approach, the binding potential of any peptide sequence (query) to the MHC molecule is determined by its similarity to a set of known peptide–MHC binders and can be obtained by comparing the query to the PSSM. Following structural considerations of the peptide–MHC interaction, we will describe here how to derive alignments and PSSMs that are suitable for the prediction of peptide–MHC binding.

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Author information

Authors and Affiliations

  1. Laboratory of Immunobiology and Department of Medical Oncology, Dana-Farber Cancer Institute; and Department of Medicine, Harvard Medical School, Boston, MA

    Pedro A. Reche

  2. Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA

    Ellis L. Reinherz

Authors
  1. Pedro A. Reche
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  2. Ellis L. Reinherz
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Editor information

Editors and Affiliations

  1. The Jenner Institute, University of Oxford, Berkshire, UK

    Darren R. Flower

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© 2007 Humana Press Inc.

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Reche, P.A., Reinherz, E.L. (2007). Prediction of Peptide-MHC Binding Using Profiles. In: Flower, D.R. (eds) Immunoinformatics. Methods in Molecular Biology™, vol 409. Humana Press. https://doi.org/10.1007/978-1-60327-118-9_13

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  • DOI: https://doi.org/10.1007/978-1-60327-118-9_13

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-699-3

  • Online ISBN: 978-1-60327-118-9

  • eBook Packages: Springer Protocols

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