Macromolecular Docking

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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 signaled by setting the ligand_centers parameter. The ligand centers may be constructed by sphgen and must reside in a file identified with the ligand_center_file parameter. See Shoichet, et al. J. Mol. Biol. 1991 for examples and discussion of macromolecular docking.

NOTE: The following parameter definitions will use the format below:

   parameter_name [default] (value):

In some cases, parameters are only needed (questions will only be asked) if the parameter above is enforced. These parameters are indicated below by additional indentation.

Orient Ligand Parameters

   * orient_ligand [yes] (yes, no):
     #Flag to orient ligand to spheres
   * automated_matching [yes] (yes, no):
     # Flag to perform automated matching instead of manual matching
         o (If automated_matching = no, then manual_matching is used)
           distance_tolerence [0.25] (float):
           #The tolerance in angstroms within which a pair of spheres is considered equivalent to
           #a pair of centers
         o distance_minimum [2.0] (float):
           #The shortest distance allowed between 2 spheres (any sphere pair with a shorter
           #distance is disregarded)
         o nodes_minimum [3] (int):
           #The minimum number of nodes in a clique
         o nodes_maximum [10] (int):
           #The maximum number of nodes in a clique
   * receptor_site_file [receptor.sph] (string):
     # The file containing the receptor spheres
   * max_orientations [500] (int):
     # The maximum number of orientations that will be cycled through
   * critical_points [no] (yes, no):
     #Flag to use critical point sphere labeling to target orientations to particular spheres
   * chemical_matching [no] (yes, no):
     #Flag to use chemical coloring of spheres to match chemical labels on ligand atoms
         o chem_match_tbl [chem_match.tbl] (string):
           #File defining the legal chemical type matches/pairings
   * use_ligand_spheres [no] (yes/no):
     #Flag to enable a sphere file representing ligand heavy atoms to be used to orient the ligand
     #Typically used for macromolecular docking
         o ligand_sphere_file [ligand.sph] (string):
           #The file containing the receptor spheres