Modeling Small Noncanonical RNA Motifs with the Rosetta FARFAR Server.
Noncanonical 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 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 Refinement (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 refinement or filtering with experimental data such as NMR chemical shifts.
Biochemistry Department, Stanford University, Stanford, CA, 94305, USA.
Joseph D
JD
Yesselman
Biochemistry Department, Stanford University, Stanford, CA, 94305, USA. rhiju@stanford.edu.|Physics Department, Stanford University, Stanford, CA, 94305, USA. rhiju@stanford.edu.
Rhiju
R
Das
D030561:Databases, Nucleic Acid; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D059372:Nucleotide Motifs; D012313:RNA / Q000737:chemistry*; D012984:Software; D014584:User-Computer Interface; D064878:Web Browser
D012313:RNA
RNA 3D structure prediction; RNA Motifs
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