Validation of a new restraint docking method for solution structure determinations of protein-ligand complexes

A new method is proposed for docking ligands into proteins in cases where a n NMR-determined solution structure of a related complex is available. The method uses a set of experimentally determined values for protein-ligand, l igand-ligand, and protein-protein restraints for residues in or near to the binding site, combined with a set of protein-protein restraints involving all the other residues which is taken from the list of restraints previousl y used to generate the reference structure of a related complex. This appro ach differs from ordinary docking methods where the calculation uses fixed atomic coordinates from the reference structure rather than the restraints used to determine the reference structure. The binding site residues influe nced by replacing the reference ligand by the new ligand were determined by monitoring differences in H-1 chemical shifts. The method has been validat ed by showing the excellent agreement between structures of L. casei dihydr ofolate reductase.trimetrexate calculated by conventional methods using a f ull experimentally determined set of restraints and those using this new re straint docking method based on an L. casei dihydrofolate reductase.methotr exate reference structure.