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.
Contents
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 Score/DOCK Cartesian Energy
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 |
