I have a related question, referring to the RosettaDock Webinar FAQ:
> Q: Is there a way of comparing affinities between ligands in Rosetta?
> The raw docking score doesn’t do a very good job at predicting affinities and is not appropriate
> for comparisons of different ligands. Rosetta -interface mode does predict delta delta G of
> binding between various ligands. However, be aware that calculating small changes in binding
> affinities is a very hard problem and the predicted changes in energies will not give a 100%
> correlation (typically ~30-60% correlation) to experimental affinities.
Is your answer the same-kind of idea, that docking program outputs *are* in fact approximations and making one of those graphs comparing affinities vs. experiments should be treated carefully? …and what did -interface mode refer to originally?