Vina Docking

This protocol uses AutoDock Vina: docking engine to predict the binding poses for a set of small molecules over the receptor. Currently, Vina 1.2 is included. 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.

Vina Docking

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.TestVina