ArticleBiophysical journal2023
Predicting 3D structures and stabilities for complex RNA pseudoknots in ion solutions.
Article in Biophysical journal, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- 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
- Tying the knot: Unraveling the intricacies of the coronavirus frameshift pseudoknot.PLoS computational biology · 2024Article
- ABC2A: A Straightforward and Fast Method for the Accurate Backmapping of RNA Coarse-Grained Models to All-Atom Structures.Molecules (Basel, Switzerland) · 2024Article
- Article
- RNA 3D Structure Prediction: Progress and Perspective.Molecules (Basel, Switzerland) · 2023Review
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5 authors.
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Abstract
RNA pseudoknots are a kind of important tertiary motif, and the structures and stabilities of pseudoknots are generally critical to the biological functions of RNAs with the motifs. In this work, we have carefully refined our previously developed coarse-grained model with salt effect through involving a new coarse-grained force field and a replica-exchange Monte Carlo algorithm, and employed the model to predict structures and stabilities of complex RNA pseudoknots in ion solutions beyond minimal H-type pseudoknots. Compared with available experimental data, the newly refined model can successfully predict 3D structures from sequences for the complex RNA pseudoknots including SARS-CoV-2 programming-1 ribosomal frameshifting element and Zika virus xrRNA, and can reliably predict the thermal stabilities of RNA pseudoknots with various sequences and lengths over broad ranges of monovalent/divalent salts. In addition, for complex pseudoknots including SARS-CoV-2 frameshifting element, our analyses show that their thermally unfolding pathways are mainly dependent on the relative stabilities of unfolded intermediate states, in analogy to those of minimal H-type pseudoknots.
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