Contact Score

From DISI
Jump to: navigation, search

The contact score is a simple summation of the number of heavy atom contacts between the ligand and receptor. At the time of construction of the contact scoring grid, the distance threshold defining a contact is set with the contact_cutoff_distance (see Grid). Atom VDW overlaps are penalized by checking the bump filter grid, or with the contact_clash_overlap parameter for the intramolecular score. The amount of penalty is specified with the contact_clash_penalty parameter.

The contact score provides a simple assessment of shape complementarity. It can be useful for evaluating primarily non-polar interactions.

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

   parameter_name [default] (value):
   #description

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.

Contact Score Parameters

   * contact_score_primary [no] (yes, no):
     #Flag to perform contact scoring as the primary scoring function
   * contact_score_secondary [no] (yes, no):
     #Flag to perform contact scoring as the secondary scoring function
         o contact_score_cutoff_distance [4.5] (float):
           #The distance threshold defining a contact
         o contact_score_clash_overlap [0.75] (float):
           #Contact definition for use with intramolecular scoring
         o contact_score_clash_penalty [50] (float):
           #The penalty for each contact overlap made
         o contact_score_grid_prefix [grid] (string):
           #The prefix to the grid files containing the desired contact
           #grid