Derivation of an amino acid similarity matrix for peptide: MHC binding and its application as a Bayesian prior.

ABSTRACT:

Background

Experts in peptide:MHC binding studies are often able to estimate the impact of a single residue substitution based on a heuristic understanding of amino acid similarity in an experimental context. Our aim is to quantify this measure of similarity to improve peptide:MHC binding prediction methods. This should help compensate for holes and bias in the sequence space coverage of existing peptide binding datasets.

Results

Here, a novel amino acid similarity matrix (PMBEC) is directly derived from the binding affinity data of combinatorial peptide mixtures. Like BLOSUM62, this matrix captures well-known physicochemical properties of amino acid residues. However, PMBEC differs markedly from existing matrices in cases where residue substitution involves a reversal of el

SUBMITTER: Kim Y 

PROVIDER: S-EPMC2790471 | biostudies-literature | 2009 Nov

REPOSITORIES: biostudies-literature