ArticlePLoS computational biology2018
Predicting 3D structure and stability of RNA pseudoknots in monovalent and divalent ion solutions.
Article in PLoS computational biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 52 citations in OpenAlex.
- gCoSRNA: Generalizable Coaxial Stacking Prediction for RNA Junctions Using Secondary Structure.Biomolecules · 2026Article
- TiRNA: a coarse-grained method with temperature and ion effects for RNA structure folding and prediction.Nucleic acids research · 2026Article
- rsRNASP1: A distance- and dihedral-dependent statistical potential for RNA 3D structure evaluation.Biophysical journal · 2025Article
- 3D structure and stability prediction of DNA with multi-way junctions in ionic solutions.PLoS computational biology · 2025Article
- Effects of Molecular Crowding on the Structure, Folding, Stability, and Catalysis of RNA.Sub-cellular biochemistry · 2025Review
- RNA Stability: A Review of the Role of Structural Features and Environmental Conditions.Molecules (Basel, Switzerland) · 2024Review
- ABC2A: A Straightforward and Fast Method for the Accurate Backmapping of RNA Coarse-Grained Models to All-Atom Structures.Molecules (Basel, Switzerland) · 2024Article
- RNA 3D Structure Prediction: Progress and Perspective.Molecules (Basel, Switzerland) · 2023Review
- Computational Modeling of DNA 3D Structures: From Dynamics and Mechanics to Folding.Molecules (Basel, Switzerland) · 2023Review
- Predicting 3D structures and stabilities for complex RNA pseudoknots in ion solutions.Biophysical journal · 2023Article
- cgRNASP: coarse-grained statistical potentials with residue separation for RNA structure evaluation.NAR genomics and bioinformatics · 2023Article
- Ab initio predictions for 3D structure and stability of single- and double-stranded DNAs in ion solutions.PLoS computational biology · 2022Article
- FebRNA: An automated fragment-ensemble-based model for building RNA 3D structures.Biophysical journal · 2022Article
- Landscape Zooming toward the Prediction of RNA Cotranscriptional Folding.Journal of chemical theory and computation · 2022Article
- rsRNASP: A residue-separation-based statistical potential for RNA 3D structure evaluation.Biophysical journal · 2022Article
- Salt-Dependent RNA Pseudoknot Stability: Effect of Spatial Confinement.Frontiers in molecular biosciences · 2021Article
- RNAStat: An Integrated Tool for Statistical Analysis of RNA 3D Structures.Frontiers in bioinformatics · 2021Article
- Salt effect on thermodynamics and kinetics of a single RNA base pair.RNA (New York, N.Y.) · 2020Article
- 3dRNA: Building RNA 3D structure with improved template library.Computational and structural biotechnology journal · 2020Article
- Structure folding of RNA kissing complexes in salt solutions: predicting 3D structure, stability, and folding pathway.RNA (New York, N.Y.) · 2019Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
RNA pseudoknots are a kind of minimal RNA tertiary structural motifs, and their three-dimensional (3D) structures and stability play essential roles in a variety of biological functions. Therefore, to predict 3D structures and stability of RNA pseudoknots is essential for understanding their functions. In the work, we employed our previously developed coarse-grained model with implicit salt to make extensive predictions and comprehensive analyses on the 3D structures and stability for RNA pseudoknots in monovalent/divalent ion solutions. The comparisons with available experimental data show that our model can successfully predict the 3D structures of RNA pseudoknots from their sequences, and can also make reliable predictions for the stability of RNA pseudoknots with different lengths and sequences over a wide range of monovalent/divalent ion concentrations. Furthermore, we made comprehensive analyses on the unfolding pathway for various RNA pseudoknots in ion solutions. Our analyses for extensive pseudokonts and the wide range of monovalent/divalent ion concentrations verify that the unfolding pathway of RNA pseudoknots is mainly dependent on the relative stability of unfolded intermediate states, and show that the unfolding pathway of RNA pseudoknots can be significantly modulated by their sequences and solution ion conditions.
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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.