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.
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
|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.
|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
|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
|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|