Though dock is typically used to process small molecules, it can be used to study the interactions of macromolecular ligands. The chief difference in protocol is that to use the match_receptor_sites procedure for the Orientation Search , then special ligand centers must be used to represent the ligand. This is signalled by setting the ligand_centers parameter. The ligand centers must reside in a file identified with the ligand_center_file parameter.
The ligand centers may be constructed with sphgen , using spheres to describe the positive image of the macromolecule. See Shoichet and Kuntz [ 26 ], for examples and discussion of macromolecular docking.
If multiple orientations are written to PDB formatted file, then the residue numbers are not disturbed. Normally, dock gives each orientation in the output PDB file a sequential residue number. However, if multiple substructures (residues) are present in the molecule input file, then this procedure is precluded.