Toward computational determination of peptide‐receptor structure

We introduce a method for docking small flexible ligands of the size of dipeptides and phosphocholine and test it against crystallographic complexes. We then show how the method can be used as the basis for a strategy for solving the much more difficult problem of docking fully flexible peptides in the 8–10‐residue size range. After developing the method we apply it to peptide–MHC class I systems and find that the predictions are in accord with biological and crystallographic data.