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
You take something like a trimer; you shove a peptide between each “point”, and boom structal change to a quadromer