Prediction of peptide-MHC binding using profiles

Methods Mol Biol. 2007;409:185-200. doi: 10.1007/978-1-60327-118-9_13.


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.

MeSH terms

  • Computational Biology
  • Databases, Protein
  • Epitopes, T-Lymphocyte / chemistry
  • Epitopes, T-Lymphocyte / metabolism
  • HLA Antigens / chemistry
  • HLA Antigens / metabolism*
  • Humans
  • Immunogenetics
  • Ligands
  • Major Histocompatibility Complex*
  • Models, Molecular
  • Protein Binding
  • Software


  • Epitopes, T-Lymphocyte
  • HLA Antigens
  • Ligands