ArticleMethods in molecular biology (Clifton, N.J.)2023
RNA 3D Modeling with FARFAR2, Online.
Article in Methods in molecular biology (Clifton, N.J.), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 9 citations in OpenAlex.
- Hierarchical breakdown of RNA structure prediction in CASP16: from reliable local helices to speculative multimer assembly.Bioinformatics (Oxford, England) · 2026Article
- Aptamer-mediated modulation of PAI-1 function reveals a novel mechanism for restoring fibrinolytic balance.NAR molecular medicine · 2026Article
- gCoSRNA: Generalizable Coaxial Stacking Prediction for RNA Junctions Using Secondary Structure.Biomolecules · 2026Article
- The Unpaved Road of Non-Coding RNA Structure-Function Relationships: Current Knowledge, Available Methodologies, and Future Trends.Non-coding RNA · 2025Review
- RNA-Puzzles Round V: blind predictions of 23 RNA structures.Nature methods · 2025Article
- Evolving Escherichia coli to use a tRNA with a non-canonical fold as an adaptor of the genetic code.Nucleic acids research · 2024Article
- The role of structure in regulatory RNA elements.Bioscience reports · 2024Review
- Comparative analysis of RNA 3D structure prediction methods: towards enhanced modeling of RNA-ligand interactions.Nucleic acids research · 2024Article
- SimRNAweb v2.0: a web server for RNA folding simulations and 3D structure modeling, with optional restraints and enhanced analysis of folding trajectories.Nucleic acids research · 2024Article
- Spatial arrangement of functional domains in OxyS stress response sRNA.RNA (New York, N.Y.) · 2023Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Understanding the three-dimensional structure of an RNA molecule is often essential to understanding its function. Sampling algorithms and energy functions for RNA structure prediction are improving, due to the increasing diversity of structural data available for training statistical potentials and testing structural data, along with a steady supply of blind challenges through the RNA-Puzzles initiative. The recent FARFAR2 algorithm enables near-native structure predictions on fairly complex RNA structures, including automated selection of final candidate models and estimation of model accuracy. Here, we describe the use of a publicly available webserver for RNA modeling for realistic scenarios using FARFAR2, available at https://rosie.rosettacommons.org/farfar2 . We walk through two cases in some detail: a simple model pseudoknot from the frameshifting element of beet western yellows virus modeled using the "basic interface" to the webserver and a replication of RNA-Puzzle 20, a metagenomic twister sister ribozyme, using the "advanced interface." We also describe example runs of FARFAR2 modeling including two kinds of experimental data: a c-di-GMP riboswitch modeled with low-resolution restraints from MOHCA-seq experiments and a tandem GA motif modeled with
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.