AutoDock-GPU Docking

This protocol uses AutoDock-GPU:, the GPU implementation of AutoDock, which is several times faster and includes many bug fixes and new features.

It includes different parameters than AutoDock4, so it has been moved to a new protocol.

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).

AutoDock-GPU Docking form 1

AutoDock-GPU 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.TestAutoDockGPU