DOCK 3.5 Score

DOCK3.5 score is a variant of Grid-based scoring (see Grid). DOCK3.5 score function calculates ligand desolvation in addition to steric and electrostatic interactions between the ligand and receptor. The electrostatic interactions between the ligand and the protein is calculated from a electrostatic potential (ESP) map. The ESP map should be calculated using finite difference Poisson-Boltzmann equation (PBE) as implemented in the program DelPhi. We provide scripts for the calculation, however DelPhi is not distributed by us.

In the DOCK scoring hierarchy DOCK3.5 Score follows GridScore and can be used both as the primary and the secondary scoring function.

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.

DOCK3.5 Score Parameters

   * dock3.5_score_primary [no] (yes, no):
     #Flag to perform dock3.5 scoring as the primary scoring function
   * dock3.5_score_secondary [no] #Flag to perform dock3.5 scoring as the secondary scoring
     #function
         o dock3.5_vdw_score [yes] (yes, no):
           #Calculate steric interaction from dock3.5 score
         o dock3.5_grd_prefix [chem52] (string):
           #Default prefix for files containing dock3.5 grids
         o dock3.5_electrostatic_score [yes] (yes, no):
           #Calculate electrostatic interaction from ESP grid calculated using DelPhi
         o dock3.5_ligand_internal_energy [no] (yes, no):
           #Flag to add ligand internal energy to the scoring function
         o dock3.5_ligand_desolvation_score [volume] (volume, total, no):
           #Calculate total or volume based ligand desolvation from solvation
           #grids
               + dock3.5_solvent_occlusion_file [solvmap] (string):
                 #Occluded solvent grid of the receptor
               + dock3.5_redistribute_positive_desolvation [no] (yes, no):
                 #positive partial atomic desolvation penalties are distributed 
         o dock3.5_occupancy_desolvation_score [no] (yes, no):
           #Calculate occupancy-based desolvation for ligand and receptor
         o dock3.5_write_atomic_energy_contribution [no] (yes, no):
           #write contribution from each atom to total score
         o dock3.5_score_vdw_scale [1.0] (float):
           #Scalar multiplier of VDW energy component
         o dock3.5_score_es_scale [1.0] (float):
           #Scalar multiplier of electrostatic energy component