title: Prediction of peptide-MHC binding using profiles.
abstract: 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.
authors.affiliation: Department of Immunology, Faculated de Medicina, Universidad Complutense de Madrid, Madrid, 28040,Spain. parecheg@med.ucm.es
authors.forename: Pedro A
authors.initials: PA
authors.lastname: Reche
authors.forename: Ellis L
authors.initials: EL
authors.lastname: Reinherz
mesh_terms: D019295:Computational Biology; D030562:Databases, Protein; D018984:Epitopes, T-Lymphocyte / Q000737:chemistry / Q000378:metabolism; D006680:HLA Antigens / Q000737:chemistry / Q000378:metabolism*; D006801:Humans; D007125:Immunogenetics; D008024:Ligands; D008285:Major Histocompatibility Complex; D008958:Models, Molecular; D011485:Protein Binding; D012984:Software
chemical_list: D018984:Epitopes, T-Lymphocyte; D006680:HLA Antigens; D008024:Ligands