Difference between revisions of "Scoring Functions"
From Rizzo_Lab
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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 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=== | ===Grid Score Parameters=== | ||
| + | {| class="wikitable" | ||
| + | |+ | ||
| + | |- | ||
| + | ! Parameter | ||
| + | ! Description | ||
| + | ! Default Value | ||
| + | |- | ||
| + | | grid_score_primary | ||
| + | | Does the user want to perform grid-based energy scoring as the primary scoring function? || yes- | ||
| + | |- | ||
| + | | ga_fraglib_scaffold_file | ||
| + | | Fragment library mol2 file containing scaffolds || - | ||
| + | |- | ||
| + | | ga_fraglib_linker_file | ||
| + | | Fragment library mol2 file containing linkers || - | ||
| + | |- | ||
===Grid Score Output Components=== | ===Grid Score Output Components=== | ||
Revision as of 12:12, 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- |
| ga_fraglib_scaffold_file | Fragment library mol2 file containing scaffolds | - |
| ga_fraglib_linker_file | Fragment library mol2 file containing linkers | - |
