Peptide-HLA Molecule Modeling Benchmark.

A set of 50 unique p-HLA complexes from the PDB was used to benchmark our modeling methodology. For each complex, the bound peptides were removed and then redocked back in to the HLA molecule. The RMSD between our solution and the experimental model is shown for the all-atom complex and the backbone-only atoms. Using each sequence, an ab initio three-dimensional model of each peptide was constructed. The ab initio peptide was then docked to the HLA molecule. The RMSD between our solution and the experimental model is shown for the all-atom and backbone-only complexes.