Output from Covalent Docking
The structural output from a covalent docking job consists of the covalently bound poses, in a Maestro file. Each pose has three main properties associated with it: the affinity score (cdock affinity), the Prime energy of the pose (Prime Energy), and an index that identifies the reactive site on the ligand if the ligand has more than one such site (ligand reaction site). Since comparing poses is only meaningful for poses bonded at the same site, you can use the index to select and compare poses for a particular ligand site. If you selected the option to calculate the Prime MM-GBSA binding affinity, this is also included as a property. The scoring properties are listed in the table below.
| Property | Description |
|---|---|
| cdock affinity | Average of the GlideScores of the pre- and post-reacted poses. Pose prediction mode only. |
| score docking score | GlideScore of the post-reacted pose. Pose prediction mode only. |
| sample docking score | GlideScore of the pre-reacted pose. |
| docking score | Best predictor of affinity, recommended for use in ranking compounds. Same as cdock affinity for pose prediction mode; same as sample docking score for screening mode |