ReviewBiochemistry2010
Robust and generic RNA modeling using inferred constraints: a structure for the hepatitis C virus IRES pseudoknot domain.
Review in Biochemistry, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 21 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
21 citing papers in PubMed.
- SHAPE Directed Discovery of New Functions in Large RNAs.Accounts of chemical research · 2021Review
- Structures and Functions of the 3' Untranslated Regions of Positive-Sense Single-Stranded RNA Viruses Infecting Humans and Animals.Frontiers in cellular and infection microbiology · 2020Review
- Progress and Current Challenges in Modeling Large RNAs.Journal of molecular biology · 2016Review
- Standing your ground to exoribonucleases: Function of Flavivirus long non-coding RNAs.Virus research · 2016Review
- Direct-Coupling Analysis of nucleotide coevolution facilitates RNA secondary and tertiary structure prediction.Nucleic acids research · 2015Article
- Messenger RNAs bearing tRNA-like features exemplified by interferon alfa 5 mRNA.Cellular and molecular life sciences : CMLS · 2015Article
- iFoldRNA v2: folding RNA with constraints.Bioinformatics (Oxford, England) · 2015Article
- RNA tertiary structure analysis by 2'-hydroxyl molecular interference.Biochemistry · 2014Article
- Topological constraints are major determinants of tRNA tertiary structure and dynamics and provide basis for tertiary folding cooperativity.Nucleic acids research · 2014Article
- Single-molecule correlated chemical probing of RNA.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Computational modeling of RNA 3D structures, with the aid of experimental restraints.RNA biology · 2014Review
- The genetic code as expressed through relationships between mRNA structure and protein function.FEBS letters · 2013Review
- Three-dimensional RNA structure refinement by hydroxyl radical probing.Nature methods · 2012Article
- RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure prediction.RNA (New York, N.Y.) · 2012Article
- Animal virus schemes for translation dominance.Current opinion in virology · 2011Review
- Crystal structure of the HCV IRES central domain reveals strategy for start-codon positioning.Structure (London, England : 1993) · 2011Article
- HCV IRES domain IIb affects the configuration of coding RNA in the 40S subunit's decoding groove.RNA (New York, N.Y.) · 2011Article
- Topological constraints: using RNA secondary structure to model 3D conformation, folding pathways, and dynamic adaptation.Current opinion in structural biology · 2011Review
- A boost for the emerging field of RNA nanotechnology.ACS nano · 2011Article
- On the significance of an RNA tertiary structure prediction.RNA (New York, N.Y.) · 2010Article
Corrections and comments
- Erratum issued
Authors and funding
4 authors.
Funding
Abstract
RNA function is dependent on its structure, yet three-dimensional folds for most biologically important RNAs are unknown. We develop a generic discrete molecular dynamics-based modeling system that uses long-range constraints inferred from diverse biochemical or bioinformatic analyses to create statistically significant (p < 0.01) nativelike folds for RNAs of known structure ranging from 45 to 158 nucleotides. We then predict the unknown structure of the hepatitis C virus internal ribosome entry site (IRES) pseudoknot domain. The resulting RNA model rationalizes independent solvent accessibility and cryo-electron microscopy structure information. The pseudoknot domain positions the AUG start codon near the mRNA channel and is tRNA-like, suggesting the IRES employs molecular mimicry as a functional strategy.
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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.