Peptide Binding Motifs for MHC Class I and II Molecules

William E. Biddison1, Roland Martin1

1 National Institute of Neurological Disorders and Stroke, NIH, Bethesda, Maryland
Publication Name:  Current Protocols in Immunology
Unit Number:  Appendix 1I
DOI:  10.1002/0471142735.ima01is36
Online Posting Date:  May, 2001
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This overview discusses the use of peptide‐bindnig motifs to predict interaction with a specific MHC class I or II allele, and gives examples for the use of MHC binding motifs to predict T‐cell recognition.

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Table of Contents

  • Using Peptide‐Binding Motifs to Predict Interaction with a Specific MHC Class I or Class II Allele
  • Examples for the Use of MHC Binding Motifs to Predict T Cell Recognition
  • Figures
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Literature Cited

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Internet Resources
  Web site for SYFPEITHI. Comprises ∼2000 peptide sequences known to bind class I and class II MHC molecules. Entries are compiled from published reports only. Very convenient to use to find binding motifs.
  Web site for MHCPEP. Lists >13,000 peptides known to bind to defined MHC molecules (Brusic et al., ).
  Web site for Bioinformatics and Molecular Analysis System (BIMAS). Contains HLA peptide binding predictions, function:rank potentials for 8‐mer, 9‐mer, or 10‐mer peptides based on predicted half‐time or dissociation to HLA class I molecules. Analysis is based on coefficient tables deduced from published literature (K. Parker, NIAID, NIH;
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