The PickPocket method for predicting binding specificities for receptors based on receptor pocket similarities: application to MHC-peptide binding.

ABSTRACT:

Motivation

Receptor-ligand interactions play an important role in controlling many biological systems. One prominent example is the binding of peptides to the major histocompatibility complex (MHC) molecules controlling the onset of cellular immune responses. Thousands of MHC allelic versions exist, making determination of the binding specificity for each variant experimentally infeasible. Here, we present a method that can extrapolate from variants with known binding specificity to those where no experimental data are available.

Results

For each position in the peptide ligand, we extracted the polymorphic pocket residues in MHC molecules that are in close proximity to the peptide residue. For MHC molecules with known specificities, we established a library of pocket-residue

SUBMITTER: Zhang H 

PROVIDER: S-EPMC2732311 | biostudies-literature | 2009 May

REPOSITORIES: biostudies-literature