Modeling small noncanonical RNA motifs with the rosetta FARFAR server

Abstract

Noncanonical RNA motifs help defi ne the vast complexity of RNA structure and function, and in many cases, these loops and junctions are on the order of only ten 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 Refi nement (FARFAR) (http://rosie.rosettacommons.org/rna_denovo/ submit) to model the 3D structure of small noncanonical RNA motifs for use in visualizing motifs and for further refi nement or fi ltering with experimental data such as NMR chemical shifts.