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-
ga_fraglib_scaffold_file	Fragment library mol2 file containing scaffolds	-
ga_fraglib_linker_file	Fragment library mol2 file containing linkers	-