Difference between revisions of "Scoring Functions"
From Rizzo_Lab
(→Grid Score Parameters) |
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| Does the user want to perform grid-based energy scoring as the primary scoring function? || yes- | | 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=== | ===Grid Score Output Components=== | ||
Revision as of 12:23, 14 April 2020
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 |
