What is the difference between “decoy” and “pose” in Rosetta?
I know conventionally “decoy” is more popular in protein docking. But it seems in Rosetta “decoy” is generalized to describe the output structure models of all Rosetta programs, not just docking results. When I read the Rosetta source code, I saw “pose” everywhere. Do they have the same concept in Rosetta?
I think you have the right idea. A pose is basically a protein conformation along with its energies. A decoy is a finished structure, but the pose is the internal c++ representation as it is being refined.