ArticleMethods in molecular biology (Clifton, N.J.)2016
Modeling Small Noncanonical RNA Motifs with the Rosetta FARFAR Server.
Article in Methods in molecular biology (Clifton, N.J.), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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8 citing papers in PubMed.
- Rapid detection of herpes simplex virus types 1 and 2 using a G-quadruplex aptamer-based biosensor.Virology journal · 2025Article
- High-throughput determination of RNA tertiary contact thermodynamics by quantitative DMS chemical mapping.Nucleic acids research · 2024Article
- Repurposing of thermally stable nucleic-acid aptamers for targeting tetrodotoxin (TTX).Computational and structural biotechnology journal · 2022Article
- Advances in RNA 3D Structure Modeling Using Experimental Data.Frontiers in genetics · 2020Review
- Assessing Exhaustiveness of Stochastic Sampling for Integrative Modeling of Macromolecular Structures.Biophysical journal · 2017Article
- F-RAG: Generating Atomic Coordinates from RNA Graphs by Fragment Assembly.Journal of molecular biology · 2017Article
- Article
- COOLAIR Antisense RNAs Form Evolutionarily Conserved Elaborate Secondary Structures.Cell reports · 2016Article
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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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