I am currently designing ligand-binding protiens, but designs are returned with more mutations than I would like. In order to reduce this number, I currently use the revert_design_to_native app, but I recently read about about the FavorNativeResidue mover. However, I am unsure of the differences in function between the two. I made two small sets of designs with the FavorNativeResidue bonus set to 0.5 and 1.5, and I ran revert_design_to_native on those designs with the same thresholds, respectivley.
i.e. input structure --> design with FavorNativeResdue bonus=n --> revert design with revert_design_to_native threshold=n
I expected that the sequences of each design and its paired revert design would be the exact same since the cutoffs were set to the same value, but they often are not. Is this because the revert_design_to_native app does a ddg calculation and the FavorNativeResidue mover calculates a different metric? The documentation for FavorNativeResidue is not clear on this as it only refers to the cutoff as a "bonus energy."
What is the difference in calculation between the two tools? If there is not one, what could account for the differences I am seeing? Lastly, are there general pros and cons associated with these tools or are there other apps/movers that would be recommended to reduce mutations based on energy?
I have attached my xml protocol below as well as a fasta with a few sequences.