Documentation of “mysterious” protocols

[Anonymous]

Hello,

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?

In Workshop #5: PyRosetta Refinement, it is pointed that ClassicRelax is the standard Rosetta refinement protocol, similar to this one (http://www.sciencemag.org/content/309/5742/1868.long); finding a paper describing the other protocols would be very nice.

Thanks.

[Anonymous]

Hi.

Tooting my own horn here, but references for all those papers can be found in this paper:
http://www.plosone.org/article/info:doi/10.1371/journal.pone.0066856

Just skim through – The section ‘Protocols Menu’ lists refs for all them (and more you may be interested in).

-Jared

[Anonymous]

Thanks Jared, this is just what I was looking for!

Changing topic status to solved.

[Anonymous]

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.

-J

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