ArticleNucleic acids research2017
Structure modeling of RNA using sparse NMR constraints.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Integrated NMR/MD investigation reveals differences after reweighting in conformational ensembles of the GAAG and GCAA tetraloops.RNA (New York, N.Y.) · 2026Article
- NMR-Based Fragment Screening for RNA-Targeted Drug Discovery.Molecules (Basel, Switzerland) · 2026Review
- The Evolving Landscape of Protein Allostery: From Computational and Experimental Perspectives.Journal of molecular biology · 2025Review
- Deciphering Dickerson-Drew DNA Equilibrium beyond the BI/BII DNA Dichotomy by Interpretation ofJournal of chemical theory and computation · 2025Article
- Prediction of 3D RNA Structures from Sequence Using Energy Landscapes of RNA Dimers: Application to RNA Tetraloops.Journal of chemical theory and computation · 2024Article
- Combining Experimental Restraints and RNA 3D Structure Prediction in RNA Nanotechnology.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Anhydrous Nucleic Acid Nanoparticles for Storage and Handling at Broad Range of Temperatures.Small (Weinheim an der Bergstrasse, Germany) · 2022Article
- Modeling Noncanonical RNA Base Pairs by a Coarse-Grained IsRNA2 Model.The journal of physical chemistry. B · 2021Article
- Developments in solution-state NMR yield broader and deeper views of the dynamic ensembles of nucleic acids.Current opinion in structural biology · 2021Review
- IsRNA1:Journal of chemical theory and computation · 2021Article
- Experimentally-driven protein structure modeling.Journal of proteomics · 2020Review
- Probing excited conformational states of nucleic acids by nitrogen CEST NMR spectroscopy.Journal of magnetic resonance (San Diego, Calif. : 1997) · 2020Article
- Limits in accuracy and a strategy of RNA structure prediction using experimental information.Nucleic acids research · 2019Article
- Computational modeling of RNA 3D structure based on experimental data.Bioscience reports · 2019Review
- Predicting 3D structure and stability of RNA pseudoknots in monovalent and divalent ion solutions.PLoS computational biology · 2018Article
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7 authors.
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Abstract
RNAs fold into distinct molecular conformations that are often essential for their functions. Accurate structure modeling of complex RNA motifs, including ubiquitous non-canonical base pairs and pseudoknots, remains a challenge. Here, we present an NMR-guided all-atom discrete molecular dynamics (DMD) platform, iFoldNMR, for rapid and accurate structure modeling of complex RNAs. We show that sparse distance constraints from imino resonances, which can be readily obtained from routine NMR experiments and easier to compile than laborious assignments of non-solvent-exchangeable protons, are sufficient to direct a DMD search for low-energy RNA conformers. Benchmarking on a set of RNAs with complex folds spanning up to 56 nucleotides in length yields structural models that recapitulate experimentally determined structures with all-heavy-atom RMSDs ranging from 2.4 to 6.5 Å. This platform represents an efficient approach for high-throughput RNA structure modeling and will facilitate analysis of diverse, newly discovered functional RNAs.
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