Given a protein complex, I would like to estimate the effect of a point mutation on the binding energy (ddG). I’d appreciate if anyone could point me to the Rosetta app(s) that I should look into. I’m fairly new to Rosetta.
I’ve asked around to see if there’s a DDG app already present in 3.2.
If not, doing it with fixbb is pretty simple:
1)Get PDBs of the bound complex and each monomer.
2)Calculate dG of binding by packing them separately subtracting their scores AB-A-B.
3)Do 2) again with the mutation in place (via resfile)
4) subtract 3 from 2 and you have ddG.