I know, there is a little bit difference between interface energy and binding energy in protein docking.
Interface energy come from, separate 2 chain (same pose) far away and then calculate total energy
Interface energy= (complex total energy) – (separated total energy)
Binding energy com from , calculate total score for each individual chain (different pose)
Binding energy = (complex total energy) – [ (individual chain 1 total energy) + (individual chain 2 total energy) ]
I would like to know, which energy is suitable to compare the binding affinity between 2 different protein to a target protein in protein docking?
Towards your question, it outputs a dG_separated value which is the value after physically separating and optionally repacking the two proteins. It would be this metric which I would recommend using for comparing binding energies of different complexes. (Along with the other metrics that get produced.)