ArticleStructure (London, England : 1993)2016
Improving NMR Structures of RNA.
Article in Structure (London, England : 1993), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
- Conformational analysis of nucleic acids for optimizing DNA and RNA topological models.Nucleic acids research · 2026Article
- DNATCO v5.0: integrated web platform for 3D nucleic acid structure analysis.Nucleic acids research · 2026Article
- Unique conformational dynamics and protein recognition of A-to-I hyper-edited dsRNA.Nucleic acids research · 2025Article
- Xplor-NIH: Better parameters and protocols for NMR protein structure determination.Protein science : a publication of the Protein Society · 2024Article
- Structural basis for high-affinity recognition of aflatoxin B1 by a DNA aptamer.Nucleic acids research · 2023Article
- Identification and characterization of RNA pentaloop sequence families.NAR genomics and bioinformatics · 2023Article
- Structural effects of m6A modification of the Xist A-repeat AUCG tetraloop and its recognition by YTHDC1.Nucleic acids research · 2022Article
- Structural insights of the conserved "priming loop" of hepatitis B virus pre-genomic RNA.Journal of biomolecular structure & dynamics · 2022Article
- Two coexisting pseudo-mirror heteromolecular telomeric G-quadruplexes in opposite loop progressions differentially recognized by a low equivalent of Thioflavin T.Nucleic acids research · 2021Article
- Targeting structural features of viral genomes with a nano-sized supramolecular drug.Chemical science · 2021Article
- NMR structural study on the self-trimerization of d(GTTAGG) into a dynamic trimolecular G-quadruplex assembly preferentially in Na+ solution with a moderate K+ tolerance.Nucleic acids research · 2021Article
- Structural basis of DNA binding to human YB-1 cold shock domain regulated by phosphorylation.Nucleic acids research · 2020Article
- A three-dimensional potential of mean force to improve backbone and sidechain hydrogen bond geometry in Xplor-NIH protein structure determination.Protein science : a publication of the Protein Society · 2020Article
- Long non-coding subgenomic flavivirus RNAs have extended 3D structures and are flexible in solution.EMBO reports · 2019Article
- Advances that facilitate the study of large RNA structure and dynamics by nuclear magnetic resonance spectroscopy.Wiley interdisciplinary reviews. RNA · 2019Review
- Structure-guided post-SELEX optimization of an ochratoxin A aptamer.Nucleic acids research · 2019Article
- Maximizing accuracy of RNA structure in refinement against residual dipolar couplings.Journal of biomolecular NMR · 2019Article
- Long-Range RNA Structural Information via a Paramagnetically Tagged Reporter Protein.Journal of the American Chemical Society · 2019Article
- Chemical and structural studies provide a mechanistic basis for recognition of the MYC G-quadruplex.Nature communications · 2018Article
- Structure of Telomerase with Telomeric DNA.Cell · 2018Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Here, we show that modern solution nuclear magnetic resonance (NMR) structures of RNA exhibit more steric clashes and conformational ambiguities than their crystallographic X-ray counterparts. To tackle these issues, we developed RNA-ff1, a new force field for structure calculation with Xplor-NIH. Using seven published NMR datasets, RNA-ff1 improves covalent geometry and MolProbity validation criteria for clashes and backbone conformation in most cases, relative to both the previous Xplor-NIH force field and the original structures associated with the experimental data. In addition, with smaller base-pair step rises in helical stems, RNA-ff1 structures enjoy more favorable base stacking. Finally, structural accuracy improves in the majority of cases, as supported by complete residual dipolar coupling cross-validation. Thus, the reported advances show great promise in bridging the quality gap that separates NMR and X-ray structures of RNA.
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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.