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Prediction of peptide-MHC binding using profiles

Reche, Pedro A and Reinherz, Ellis L (2007) Prediction of peptide-MHC binding using profiles. Methods in molecular biology (Clifton, N.J.), 409 . pp. 185-200. ISSN 1064-3745

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Official URL: http://www.springer.com/series/7651

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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.


Item Type:Article
Uncontrolled Keywords:PSSM; MHC; Binding; Epitopes; Profile; Prediction
Subjects:Medical sciences > Medicine > Immunology
Sciences > Computer science > Bioinformatics
Medical sciences > Biology > Molecular biology
ID Code:9325
Deposited On:06 Aug 2009 08:02
Last Modified:06 Feb 2014 08:23

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