Prediction of Peptide-MHC Binding Using Profiles

• DOI: 10.1007/978-1-60327-118-9_13
• Publication Date: 2007-06-14T16:39:53Z
• Authors: Pedro A. Reche; Ellis L. Reinherz
• Keywords: 612.017; 0301 basic medicine; Models, Molecular; 2412 Inmunología; Inmunología; 2415 Biología Molecular; Epitopes, T-Lymphocyte; Ligands; 57:004; Major Histocompatibility Complex; PSSM; Epitopes; 03 medical and health sciences; 0302 clinical medicine; HLA Antigens; Immunogenetics; Humans; Databases, Protein; Biología molecular; Biología molecular (Biología); Computational Biology; Bioinformática; Binding; Profile; MHC; Prediction; Software; Protein Binding

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.