UNIT 18.17 The MHC Motif Viewer: A Visualization Tool for MHC Binding Motifs

  1. Nicolas Rapin1,
  2. Ilka Hoof2,3,
  3. Ole Lund3,
  4. Morten Nielsen3

Published Online: 1 FEB 2010

DOI: 10.1002/0471142735.im1817s88

Current Protocols in Immunology

Current Protocols in Immunology

How to Cite

Rapin, N., Hoof, I., Lund, O. and Nielsen, M. 2010. The MHC Motif Viewer: A Visualization Tool for MHC Binding Motifs. Current Protocols in Immunology. 88:18.17:18.17.1–18.17.13.

Author Information

  1. 1

    Department of Pharmaceutics and Analytical Chemistry, Faculty of Pharmaceutical Sciences, University of Copenhagen, Copenhagen, Denmark

  2. 2

    Department of Theoretical Biology/Bioinformatics, Utrecht University, Utrecht, The Netherlands

  3. 3

    Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark

Publication History

  1. Published Online: 1 FEB 2010
  2. Published Print: FEB 2010


In vertebrates, the onset of cellular immune reactions is controlled by presentation of peptides in complex with major histocompatibility complex (MHC) molecules to T cell receptors. In humans, MHCs are called human leukocyte antigens (HLAs). Different MHC molecules present different subsets of peptides, and knowledge of their binding specificities is important for understanding differences in the immune response between individuals. Algorithms predicting which peptides bind a given MHC molecule have recently been developed with high prediction accuracy. The utility of these algorithms is hampered by the lack of tools for browsing and comparing specificity of these molecules. We have developed a Web server, MHC Motif Viewer, which allows the display of the binding motif for MHC class I proteins for human, chimpanzee, rhesus monkey, mouse, and swine, as well as HLA-DR protein sequences. The binding motif for each MHC molecule is predicted using state-of-the-art, pan-specific peptide-MHC binding-prediction methods, and is visualized as a sequence logo, in a format that allows for a comprehensive interpretation of binding motif anchor positions and amino acid preferences. Curr. Protoc. Immunol. 88:18.17.1-18.17.13. © 2010 by John Wiley & Sons, Inc.


  • MHC;
  • HLA;
  • T cell epitope;
  • binding motif;
  • binding specificity;
  • viewer