I have read the paper "Protein-Protein Docking with Backbone Flexibility" and would like to perform protein-protein docking with loop flexibility as described in the paper. I have also found the forum post https://www.rosettacommons.org/guide/Pose%20Docking , which describes how to run the protocols. Unfortunately, the commands only work for the old 2.x Rosetta versions and therefore I would like to know if those protocols are also available for the 3.x versions, which I may have missed. If not, is there any tips how to transform the protocols from the old to the new version without much hassle.
Thank you very much!