Limitations of Ab initio predictions of peptide binding to MHC class II molecules.

ABSTRACT: Successful predictions of peptide MHC binding typically require a large set of binding data for the specific MHC molecule that is examined. Structure based prediction methods promise to circumvent this requirement by evaluating the physical contacts a peptide can make with an MHC molecule based on the highly conserved 3D structure of peptide:MHC complexes. While several such methods have been described before, most are not publicly available and have not been independently tested for their performance. We here implemented and evaluated three prediction methods for MHC class II molecules: statistical potentials derived from the analysis of known protein structures; energetic evaluation of different peptide snapshots in a molecular dynamics simulation; and direct analysis of contacts made in

SUBMITTER: Zhang H 

PROVIDER: S-EPMC2822856 | biostudies-literature | 2010 Feb

REPOSITORIES: biostudies-literature