AutoDock4 Docking

This protocol uses AutoDock4: tool to predict the binding poses for a set of small molecules over the receptor.

The search parameters can be modified to make a full use of the AutoDock4 options.

The input can either be an AtomStruct (to perform the docking on the whole protein) or a SetOfStructROIs (to perform the docking only on the Structural Regions Of Interest).

Input

Note

All parameters include a help button that gives further information for each of them.

AutoDock4 Docking form 1

AutoDock4 Docking form 2

The results of these protocols are a SetOfSmallMolecules, containing the predicted binding poses for the input molecules. The user can visualize them using Analyze Results, which will display the General SmallMolecules viewer.

A section for defining flexible receptor residues is included in these docking protocols.

Test

This protocol has an integrated test that can be run using the following command:

scipion3 tests autodock.tests.test_autodock.TestAutoDock