ArticleNucleic acids research2014
The role of nucleobase interactions in RNA structure and dynamics.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 87 papers.
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Who cites it
87 citing papers in PubMed.
- From gHBfix to NBfix: Reweighting-Driven Refinement of Hydrogen-Bond Interactions in RNA Force Fields.Journal of chemical theory and computation · 2026Article
- Conformational landscape of 2-aminopurine-substituted RNA oligonucleotides from machine-learning-driven enhanced sampling.Physical chemistry chemical physics : PCCP · 2026Article
- Molecular Interpretation of Temperature-Induced DNA Melting Monitored through Base Dipole Moment Changes as a Surrogate of the Hypochromic Shift.The journal of physical chemistry letters · 2026Article
- Integrated NMR/MD investigation reveals differences after reweighting in conformational ensembles of the GAAG and GCAA tetraloops.RNA (New York, N.Y.) · 2026Article
- Unraveling the Mechanism of Drug Binding to SARS-CoV-2 RNA Pseudoknot With Thermodynamics-Driven Machine Learning.Journal of computational chemistry · 2026Article
- miR-155-SOCS1-Telomere Length Axis: A Tripartite and Multifaceted Approach To Understanding Rheumatoid Arthritis Pathophysiology.Cell biochemistry and biophysics · 2026Article
- Reparameterization of the Amber RNA Force Field Non-Bonded Terms.bioRxiv : the preprint server for biology · 2026Article
- U2 snRNP recognizes the branch site through a loaded-spring strand-invasion mechanism.Nucleic acids research · 2026Article
- Critical Assessment of a Structure-Based Pipeline for Targeting the Long Noncoding RNA MALAT1.Journal of chemical information and modeling · 2026Article
- Spectral Graph Features for Reference-free RNA 3D Quality Assessment.bioRxiv : the preprint server for biology · 2026Article
- FRET-guided selection of RNA 3D structures.Nucleic acids research · 2026Article
- Latent thermodynamic flows: unified representation learning and generative modeling of temperature-dependent behaviors from limited data.Chemical science · 2026Article
- Article
- Critical structural perturbations of ribozyme active sites induced by 2'-O-methylation commonly used in structural studies.Nucleic acids research · 2026Article
- RNAdvisor 2: A unified platform for RNA 3D model quality assessment using metrics, scoring functions, and meta-metrics.Scientific reports · 2025Article
- Molecular properties and intramolecular interactions of peptide-conjugated phosphorodiamidate morpholino oligonucleotides.Molecular therapy. Nucleic acids · 2025Article
- RNA G-quadruplexes emerge from a compacted coil-like ensemble via multiple pathways.Nucleic acids research · 2025Article
- Graph neural network and diffusion model for modeling RNA interatomic interactions.Bioinformatics (Oxford, England) · 2025Article
- Targeting Glioblastoma Stem Cells via EphA2: Structural Insights into the RNA Aptamer A40s for Precision Therapy.Journal of chemical information and modeling · 2025Article
- Ensemble refinement of mismodeled cryo-EM RNA structures using all-atom simulations.Nature communications · 2025Article
27 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The intricate network of interactions observed in RNA three-dimensional structures is often described in terms of a multitude of geometrical properties, including helical parameters, base pairing/stacking, hydrogen bonding and backbone conformation. We show that a simple molecular representation consisting in one oriented bead per nucleotide can account for the fundamental structural properties of RNA. In this framework, canonical Watson-Crick, non-Watson-Crick base-pairing and base-stacking interactions can be unambiguously identified within a well-defined interaction shell. We validate this representation by performing two independent, complementary tests. First, we use it to construct a sequence-independent, knowledge-based scoring function for RNA structural prediction, which compares favorably to fully atomistic, state-of-the-art techniques. Second, we define a metric to measure deviation between RNA structures that directly reports on the differences in the base-base interaction network. The effectiveness of this metric is tested with respect to the ability to discriminate between structurally and kinetically distant RNA conformations, performing better compared to standard techniques. Taken together, our results suggest that this minimalist, nucleobase-centric representation captures the main interactions that are relevant for describing RNA structure and dynamics.
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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.