I have generated protein-protein decoys using ZDock and I am trying to rank them using ZRank scoring function. I was not clear about what was mentioned in the ZRank read-me file.
After generating the decoys using ZDock, do I add polar hydrogens to all of the decoys or only the unbound structures ?
From what is mentioned in the Readme file, I assume that polar hydrogens need to be added only to the unbound structures. However could anyone confirm this?