Modeling Small Noncanonical RNA Motifs with the Rosetta FARFAR Server

Joseph D Yesselman; Rhiju Das

doi:10.1007/978-1-4939-6433-8_12

Modeling Small Noncanonical RNA Motifs with the Rosetta FARFAR Server

Methods Mol Biol. 2016:1490:187-98. doi: 10.1007/978-1-4939-6433-8_12.

Authors

Joseph D Yesselman¹, Rhiju Das^{2

3}

Affiliations

¹ Biochemistry Department, Stanford University, Stanford, CA, 94305, USA.
² Biochemistry Department, Stanford University, Stanford, CA, 94305, USA. [email protected].
³ Physics Department, Stanford University, Stanford, CA, 94305, USA. [email protected].

Abstract

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.

Keywords: RNA 3D structure prediction; RNA Motifs.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Databases, Nucleic Acid*
Models, Molecular*
Nucleic Acid Conformation*
Nucleotide Motifs*
RNA / chemistry*
Software*
User-Computer Interface
Web Browser

Substances

RNA

Abstract

Publication types

MeSH terms

Substances

Grants and funding