| Chapter title |
Modeling Small Noncanonical RNA Motifs with the Rosetta FARFAR Server
|
|---|---|
| Chapter number | 12 |
| Book title |
RNA Structure Determination
|
| Published in |
Methods in molecular biology, January 2016
|
| DOI | 10.1007/978-1-4939-6433-8_12 |
| Pubmed ID | |
| Book ISBNs |
978-1-4939-6431-4, 978-1-4939-6433-8
|
| Authors |
Joseph D. Yesselman, Rhiju Das |
| 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. |
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|---|---|---|
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Demographic breakdown
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|---|---|---|
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| Professor | 4 | 20% |
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| Student > Ph. D. Student | 1 | 5% |
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|---|---|---|
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| Other | 0 | 0% |
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