I am trying to find where, in all Rosetta versions available, one can access the Knotfind algorithm described in this publication:
https://www.researchgate.net/profile/Matthew-Weirauch/publication/6913921_Rapid_knot_detection_and_application_to_protein_structure_prediction/links/00b7d522773fa9f74c000000/Rapid-knot-detection-and-application-to-protein-structure-prediction.pdf
Does anyone know which Rosetta version contains it?
Category:
Post Situation:
It looks like that protocol was implemented in Rosetta++ (Rosetta2) and was never ported over to Rosetta3.
Rosetta2 should be availible on the Rosetta download page (though you may have to search for it -- "Rosetta 2.3.1" is mixed in with the Rosetta3 releases on the academic download page.)
Please note that it's been over a decade since Rosetta 2 was last released, so there may be issues compiling and running it on modern machines, and there's not really any current experience with running it. You can try, but it just be forewarned that it may take some effort to get working.