Scoring Functions

DOCK uses several types of scoring functions to discriminate among orientations and molecules. Scoring is requested using the score_molecules parameter. A large portion of scoring functions can be called through descriptor score (but not all). Those with descriptor score functionality will be denoted as such.

Grid-Based Score

DOCK needs a fast scoring function to evaluate poses rapidly during growth. The energy grid is used for this. The grid stores the non-bonded Molecular Mechanics Potential of the receptor at each grid point.

Grid can be called under descriptor score but it is suggested to not mix grid-based and cartesian space as that will dramatically increase computing time.

Grid Score Parameters

Parameter	Description	Default Value
grid_score_primary	Does the user want to perform grid-based energy scoring as the primary scoring function?	yes-
grid_score_rep_rad_scale	Scalar multiplier of the radii for the repulsive portion of the VDW energy component only when grid score is turned on	1.0
grid_score_vdw_scale	Scalar multiplier of the VDW energy component	1
grid_score_turn_off_vdw	A flag to turn off vdw portion of scoring function when grid score vdw scale = 0	yes
grid_score_es_scale	Flag to scale up or down the es portion of the scoring function when es scale is turned on	1
grid_score_turn_off_es	A flag to turn off es portion of scoring function when grid score es scale = 0	yes
grid_score_grid_prefix	The prefix to the grid files containing the desired nrg/bmp grid	grid

Grid Score Output Components

These values will be printed in the header of the mol2 file post DOCK process.

Output Component	Description
Grid_score	Sum of the VDW and ES interactions
Grid_vdw_energy	VDW interaction between the ligand grid
Grid_es_energy	ES interaction betweent eh ligand and grid

Continuous/DOCK Cartesian Energy Score

Continuous scoring may be used to evaluate a ligand:receptor complex without the investment of a grid calculation, or to perform a more detailed calculation without the numerical approximation of the grid. Continuous score is implemented under Descriptor Score as well. Continuous score is a cartesian based score and can be combined with other Cartesian based scores with very little computational expense.

Continuous/DCE Score Parameters

Parameter	Description	Default Value
continuous_score_primary	Does the user want to perform continuous non-grid scoring as the primary scoring function?	no
continuous_score_secondary	Does the user want to perform continuous non-grid scoring as the secondary scoring function?	no
cont_score_rec_filename	File that contains receptor coordinates	receptor.mol2
cont_score_att_exp	VDW Lennard-Jones potential attractive exponent	6
cont_score_rep_exp	VDW Lennard-Jones potential repulsive exponent	12
cont_score_rep_rad_scale	Scalar multiplier of the radii for the repulsive portion of the vdw energy component only	1.0
cont_score_use_dist_dep_dielectric	Distance dependent dielectric switch	yes
cont_score_dielectric	Dielectric constant for the electrostatic term
cont_score_vdw_scale	Scalar multiplier of vdw energy component	1
cont_score_vdw_scale	Flag to turn off vdw portion of the scoring function when cont_score_vdw_scale=0	yes
cont_score_es_scale	Scalar multiplier of electrostatic energy component	1.0
cont_score_turn_off_es	Flag to turn off es portion of the scoring function when cont_score_es_scale = 0	yes

Continuous/DCE Score Output Components

Output Component	Description
Continuous-score	sum of the van der Waals and electrostatic interactions
Continuous_vdw_energy	VDW interaction between ligand and receptor
Continuous_es_energy	ES interaction between the ligand and receptor