P2Rank pocket prediction

The main program of the P2Rank package is P2Rank and it is integrated in Scipion-chem-p2rank as a protocol.

P2Rank pocket prediction protocol

Input

This protocol takes a AtomStruct as an input and predicts its pockets based on a machine learning model over its surface.

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 P2Rank page.

P2Rank pocket prediction form

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 p2rank.tests.test_p2rank.TestP2Rank

Viewer

The viewer for p2rank results include the Pymol General Viewer for SetOfStructROIs objects plus an specific viewer of the surface points visualization they provide.


P2Rank pocket prediction viewer P2Rank pocket prediction 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.