In the tutorial, how do we assess if the CAPRI quality has improved in scenario 2 compared to scenario 1? Is there an explicit way to find out or do we need to perform some prior calculations?
You can of course only assess this if you know the correct answer…
And then calculate the interface RMSDs, ligand RMSD and fraction of native contacts.
Useful software for doing this is DockQ: https://github.com/bjornwallner/DockQ