Dear all,
I would like to know which scoring function is using the docking protocol in Rosie. I guess is the last one (ref2015) but I couldn't find any reference. Also looking to the documentation online (http://rosie.rosettacommons.org/docking2/documentation) reading the papers I'm not 100% sure of the specific protocol, is it the same as a local docking in Rosetta? or are there any step changed? (https://www.rosettacommons.org/demos/latest/tutorials/Protein-Protein-Docking/Protein-Protein-Docking#local-docking) I am asking this because I would like to reproduce some of my results locally ( although I know is a stochastic process I want to increase the number of decoys).
Thanks in advance
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Hello,
The current docking protocol has a hard coded score function for the high res cycle, which is the docking with docking_min patch. Since this hasn't changed for a few years, I would expect the server to use the same score function. Sergey can confirm this. We are in the process of transitioning to REF2015.
Hope this helps.
Shourya