I have read the paper "Protein-Protein Docking with Backbone Flexibility" and would like to perform protein-protein docking with loop rebuilding as described in the paper. During this special process, the loop region was rebuilt after the low-resolution docking, and then the sidechains were added back and the full-atom structure was refined by "a protocol in which rigid-backbone MCM docking alternates with loop modeling by MC CCD minimization". Unfortunately, the paper didn't give the details or commands for how to run this special docking process within rosetta suite.
Is it possible to achieve this process by using a single protocol? or should I use several independent protocols, by taking the output of one protocol as the input of another one?
Thanks a lot!