Rosetta is a set of physical-based protein folding models. protein binding with Rosetta check a protein surface check how protein side-chains interact with the binding surface peptide binding with Rosetta The difficulty with this is that we don’t know what the overall tertiary structure of a group of peptides are; unlike whole protein binding. sequence-specific DNA binding ??? more! You take something like a trimer; you shove a peptide between each “point”, and boom structal change to a quadromer