I am a new user to Rosetta and i have a question regrading the relax protocol. I have been using it to create decoys for a target protein, however, I get a sense that the configurations that I am getting are too close to the original structure and so I am not getting a good enough sampling of the conformational space. Is there another protocol I can try or maybe a flag to be used inside the relax protocol to get a more rigorous sampling?
You want to use the Backrub Application to create an ensemble of structures for your target protein.
Check it out here:
There is also a server for it as well from the Kortemme Lab:
You may also be able to use ab initio folding to generate a wider ensemble.