Files supporting a protocol for FMDV homology modeling from EMCV
If you have access to Rosetta -- academic software for biomolecular modeling, with programs especially suited to RNA structure modeling -- you may wish to follow along with the attached inputs and annotated executable scripts.
If you don't have access to Rosetta, catch up -- if you're interested in this topic, you should get modeling with Rosetta! The academic license is free and the commercial license is priced in a manner I am told is compassionate towards small startups.
Publication details for the primary citation of this work will follow. In the meantime, two Rosetta components for RNA modeling feature heavily in this work:
stepwise Monte Carlo (stepwise or SWM): Watkins, AM et al. Blind prediction of noncanonical RNA structure at atomic accuracy. Science Advances 2018, 4 (5), eaar5316. DOI: 10.1126/sciadv.aar5316
Fragment Assembly of RNA with Full-Atom Refinement (FARFAR): Das R, Karanikolas J, Baker D. Atomic accuracy in predicting and designing noncanonical RNA structure. Nat Methods 2010, 7 (4), 291-4. DOI: 10.1038/nmeth.1433