Compound Docking/Scoring

Predict the geometry (pose) and strength (affinity) of small-molecule binding.

Menu: Binding → Docking → Perform Docking/Scoring

This plugin uses a version of AutoDock Vina (Webina) to perform the docking calculations.

Where to find it

Parameter	Default	Description
`makemolinputparams`	—	—
`region`	—	—
Number of processors	`15`	The number of processors to use for docking.
Exhaustiveness	`UserArgType.Checkbox`	How thoroughly to search for the pose. Roughly proportional to time.
Maximum rotatable bonds	`15`	Compounds with too many rotatable bonds will be skipped to avoid excessive run times and less accurate predictions.
Score existing poses, without redocking	No	Scores existing docked or crystallographic poses, without repositioning compounds.
Keep only highest-scoring pose for each compound	Yes	Docking generates multiple poses; the top-scoring pose is often correct, but sometimes alternatives may be more accurate.

Unless you are an expert user, these advanced parameters are best left unmodified.

Parameter	Default	Description
Seed	`UserArgType.TextArea`	The explicit seed. Useful if reproducibility is critical.
Number of modes	`UserArgType.Vector3D`	The maximum number of binding poses to show.
Energy range	`UserArgType.Color`	The maximum energy difference between the best and worst pose.