I’ve been using PyRosetta’s pre-packed protocols like ClassicRelax, FastRelax and LoopMover_Refine_CCD thoroughly, but I’ve been unable to find documentation of these. I would like to know which steps are taken by these protocols in order to complete their tasks; if such information is available, could someone link me to it?
Great! Yeah, the FastRelax paper especially – I didn’t even know there was a paper on it till a few months ago.
You should also checkout http://www.rosettacommons.org/manual_guide ; specifically both 3.4 and 3.5 docs. Most of the apps, like docking or loop modeling are exposed in PyRosetta as you’ve seen and have more docs and references in the full Rosetta manual.