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Modeling Small Non-canonical RNA Motifs with the Rosetta FARFAR Server

Non-canonical RNA motifs help define the vast complexity of RNA structure and function, and in many cases, these loops and junctions are on the order of only 10 nucleotides in size. Unfortunately, despite their small size, there is no reliable method to determine the ensemble of lowest energy structures of junctions and loops at atomic accuracy. This chapter outlines straightforward protocols using a webserver for Rosetta Fragment Assembly of RNA with Full Atom Refinement (FARFAR) (http://rosie.rosettacommons.org/rna_denovo/submit) to model the 3D structure of small non-canonical RNA motifs for use in visualizing motifs and for further refinement or filtering with experimental data such as NMR chemical shifts.