ReviewRNA (New York, N.Y.)2018
Challenges and approaches to predicting RNA with multiple functional structures.
Review in RNA (New York, N.Y.), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Deep Learning in Modeling Tools for Structural Insights into Protein-RNA Complexes, Bridging Computational and Spectroscopic Approaches.Methods in molecular biology (Clifton, N.J.) · 2026Article
- A conserved RNA structure at the capsid-coding sequence of Zika virus genome is required for viral replication in a host-dependent manner.Journal of virology · 2025Article
- Selective [9-Chembiochem : a European journal of chemical biology · 2025Article
- RNA fold prediction by Monte Carlo in graph space and the statistical mechanics of tertiary interactions.RNA (New York, N.Y.) · 2024Article
- Systematic benchmarking of deep-learning methods for tertiary RNA structure prediction.PLoS computational biology · 2024Article
- Kinetic pathway of HIV-1 TAR cotranscriptional folding.Nucleic acids research · 2024Article
- Functional microRNA-targeting drug discovery by graph-based deep learning.Patterns (New York, N.Y.) · 2024Article
- A Hitchhiker's guide to RNA-RNA structure and interaction prediction tools.Briefings in bioinformatics · 2023Review
- Unraveling the Enzyme-Substrate Properties for APOBEC3A-Mediated RNA Editing.Journal of molecular biology · 2023Article
- RNA folding pathways from all-atom simulations with a variationally improved history-dependent bias.Biophysical journal · 2023Article
- RNA levers and switches controlling viral gene expression.Trends in biochemical sciences · 2023Review
- The Energy Landscape Perspective: Encoding Structure and Function for Biomolecules.Frontiers in molecular biosciences · 2022Article
- Article
- Targeting RNA structures in diseases with small molecules.Essays in biochemistry · 2020Review
- On the Problem of Reconstructing a Mixture of RNA Structures.Bulletin of mathematical biology · 2020Article
- Review
- RNA Secondary Structure Motifs of the Influenza A Virus as Targets for siRNA-Mediated RNA Interference.Molecular therapy. Nucleic acids · 2020Article
- Article
- Probing RNA structure in vivo.Current opinion in structural biology · 2019Review
- The roles of structural dynamics in the cellular functions of RNAs.Nature reviews. Molecular cell biology · 2019Review
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1 author.
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No grant is acknowledged in the PubMed record.
Abstract
The revolution in sequencing technology demands new tools to interpret the genetic code. As in vivo transcriptome-wide chemical probing techniques advance, new challenges emerge in the RNA folding problem. The emphasis on one sequence folding into a single minimum free energy structure is fading as a new focus develops on generating RNA structural ensembles and identifying functional structural features in ensembles. This review describes an efficient combinatorially complete method and three free energy minimization approaches to predicting RNA structures with more than one functional fold, as well as two methods for analysis of a thermodynamics-based Boltzmann ensemble of structures. The review then highlights two examples of viral RNA 3'-UTR regions that fold into more than one conformation and have been characterized by single molecule fluorescence energy resonance transfer or NMR spectroscopy. These examples highlight the different approaches and challenges in predicting structure and function from sequence for RNA with multiple biological roles and folds. More well-defined examples and new metrics for measuring differences in RNA structures will guide future improvements in prediction of RNA structure and function from sequence.
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Registered trials
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.