ArticleProceedings of the National Academy of Sciences of the United States of America2014
Graph-based sampling for approximating global helical topologies of RNA.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers.
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Who cites it
48 citing papers in PubMed.
- Open questions on viral frameshifting: Exploiting the structural plasticity of the frameshifting element for therapeutic intervention.Biophysical journal · 2026Review
- How large is the universe of RNA-like motifs? A clustering analysis of RNA graph motifs using topological descriptors.PLoS computational biology · 2025Article
- RNA fold prediction by Monte Carlo in graph space and the statistical mechanics of tertiary interactions.RNA (New York, N.Y.) · 2024Article
- Sampling globally and locally correct RNA 3D structures using Ernwin, SPQR and experimental SAXS data.Nucleic acids research · 2024Article
- RNAJP: enhanced RNA 3D structure predictions with non-canonical interactions and global topology sampling.Nucleic acids research · 2023Article
- RNA-As-Graphs Motif Atlas-Dual Graph Library of RNA Modules and Viral Frameshifting-Element Applications.International journal of molecular sciences · 2022Article
- rsRNASP: A residue-separation-based statistical potential for RNA 3D structure evaluation.Biophysical journal · 2022Article
- Computational tools to study RNA-protein complexes.Frontiers in molecular biosciences · 2022Review
- Diagrammatic approaches to RNA structures with trinucleotide repeats.Biophysical journal · 2021Article
- Structure-altering mutations of the SARS-CoV-2 frameshifting RNA element.Biophysical journal · 2021Article
- RNA 3D Structure Prediction Using Coarse-Grained Models.Frontiers in molecular biosciences · 2021Review
- Predicting RNA Scaffolds with a Hybrid Method of Vfold3D and VfoldLA.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Salt-Dependent RNA Pseudoknot Stability: Effect of Spatial Confinement.Frontiers in molecular biosciences · 2021Article
- Structure-Altering Mutations of the SARS-CoV-2 Frame Shifting RNA Element.bioRxiv : the preprint server for biology · 2020Article
- Topological constraints of RNA pseudoknotted and loop-kissing motifs: applications to three-dimensional structure prediction.Nucleic acids research · 2020Article
- Identification of novel RNA design candidates by clustering the extended RNA-As-Graphs library.Biochimica et biophysica acta. General subjects · 2020Article
- Inverse folding with RNA-As-Graphs produces a large pool of candidate sequences with target topologies.Journal of structural biology · 2020Article
- RAG-Web: RNA structure prediction/design using RNA-As-Graphs.Bioinformatics (Oxford, England) · 2020Article
- Structure folding of RNA kissing complexes in salt solutions: predicting 3D structure, stability, and folding pathway.RNA (New York, N.Y.) · 2019Article
- VfoldLA: A web server for loop assembly-based prediction of putative 3D RNA structures.Journal of structural biology · 2019Article
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Authors and funding
6 authors.
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Abstract
A current challenge in RNA structure prediction is the description of global helical arrangements compatible with a given secondary structure. Here we address this problem by developing a hierarchical graph sampling/data mining approach to reduce conformational space and accelerate global sampling of candidate topologies. Starting from a 2D structure, we construct an initial graph from size measures deduced from solved RNAs and junction topologies predicted by our data-mining algorithm RNAJAG trained on known RNAs. We sample these graphs in 3D space guided by knowledge-based statistical potentials derived from bending and torsion measures of internal loops as well as radii of gyration for known RNAs. Graph sampling results for 30 representative RNAs are analyzed and compared with reference graphs from both solved structures and predicted structures by available programs. This comparison indicates promise for our graph-based sampling approach for characterizing global helical arrangements in large RNAs: graph rmsds range from 2.52 to 28.24 Å for RNAs of size 25-158 nucleotides, and more than half of our graph predictions improve upon other programs. The efficiency in graph sampling, however, implies an additional step of translating candidate graphs into atomic models. Such models can be built with the same idea of graph partitioning and build-up procedures we used for RNA design.
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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.