TOWARD COMPUTATIONAL DETERMINATION OF PEPTIDE-RECEPTOR STRUCTURE

We introduce a method for docking small flexible ligands of the size o f dipeptides and phosphocholine and test it against crystallographic c omplexes. We then show how the method can be used as the basis for a s trategy for solving the much more difficult problem of docking fully f lexible 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 pr edictions are in accord with biological and crystallographic data.