UNIT 18.17 The MHC Motif Viewer: A Visualization Tool for MHC Binding Motifs
Published Online: 1 FEB 2010
Copyright © 2010 by John Wiley & Sons, Inc.
Lab Protocol Title
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.
- Published Online: 1 FEB 2010
- 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.
- T cell epitope;
- binding motif;
- binding specificity;