Pocket prediction

The main program of the FPocket package is fpocket and it is integrated in scipion-chem-fpocket as a protocol.

This protocol takes a AtomStruct as an input and predicts its pockets based on its concavities (based on alpha-spheres) and electrostatics. The parameters in the form control the alpha-spheres creation and their posterior clustering.

Input

Note

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

If you need more information we recommend you to check the FPocket documentation.

The result of this protocol is a SetOfStructROIs object, containing the predicted pockets. You can inspect this pockets using the Analyze results button or if you want to directly see the related files you will be able to find them in the protocol’s folder.

Test

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

scipion3 tests fpocket.tests.test_fpocket.TestFPocket

Viewer

The viewer for fpocket results include the Pymol General Viewer for SetOfStructROIs objects plus an specific viewer of the alpha-spheres over the protein structure using VMD.

As for the rest of the Scipion object, you can also check Table view to visualize the stored parameters for each of the items in the set.