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!
The paper was performed with Rosetta++, so command details probably wouldn't help running with Rosetta3, anyway.
I'm not sure that the protocol is exactly the same, but to use a similar sort of flexible modeling, you would want to use the "-docking:use_legacy_protocol" mode of the the docking_protocol application with the -docking:flexible_bb_docking option. (The DockingProtocol mover in RosettaScripts should also obey those command line options.)
Reasonable options of the latter include "ccd", "kic" and "backrub". The Wang paper would be the "ccd", unless I miss my guess. Keep in mind that like the other CCD loop remodeling in Rosetta you'll need to supply a loops file and fragments (see https://www.rosettacommons.org/docs/wiki/application_documentation/struc... and https://www.rosettacommons.org/docs/wiki/application_documentation/struc...).