ArticleRNA (New York, N.Y.)2005
Predicting RNA folding thermodynamics with a reduced chain representation model.
Article in RNA (New York, N.Y.), 2005. 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.
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- Hierarchical breakdown of RNA structure prediction in CASP16: from reliable local helices to speculative multimer assembly.Bioinformatics (Oxford, England) · 2026Article
- Computational approaches for RNA structure prediction and design.Cell reports. Physical science · 2026Article
- Kinetic Traps in RNA Folding: Targeted Design of Frameshifting Element Mutants by Thermodynamic and Kinetic Analysis of the Chikungunya Virus.The journal of physical chemistry. B · 2026Article
- rsRNASP1: A distance- and dihedral-dependent statistical potential for RNA 3D structure evaluation.Biophysical journal · 2025Article
- Molecular Crowding by Computational Approaches.Sub-cellular biochemistry · 2025Review
- Transformers in RNA structure prediction: A review.Computational and structural biotechnology journal · 2025Review
- Systematic benchmarking of deep-learning methods for tertiary RNA structure prediction.PLoS computational biology · 2024Article
- Kinetic pathway of HIV-1 TAR cotranscriptional folding.Nucleic acids research · 2024Article
- State-of-the-RNArt: benchmarking current methods for RNA 3D structure prediction.NAR genomics and bioinformatics · 2024Article
- Advancing RNA 3D structure prediction: Exploring hierarchical and hybrid approaches in CASP15.Proteins · 2023Article
- trRosettaRNA: automated prediction of RNA 3D structure with transformer network.Nature communications · 2023Article
- RNA Folding Based on 5 Beads Model and Multiscale Simulation.Interdisciplinary sciences, computational life sciences · 2023Article
- Mono-valent salt corrections for RNA secondary structures in the ViennaRNA package.Algorithms for molecular biology : AMB · 2023Article
- 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
- cRNAsp12 Web Server for the Prediction of Circular RNA Secondary Structures and Stabilities.International journal of molecular sciences · 2023Article
- Structural, Dynamical, and Entropic Differences between SARS-CoV and SARS-CoV-2 s2m Elements Using Molecular Dynamics Simulations.ACS physical chemistry Au · 2023Article
- RNA 3D Modeling with FARFAR2, Online.Methods in molecular biology (Clifton, N.J.) · 2023Article
- 3dDNA: A Computational Method of Building DNA 3D Structures.Molecules (Basel, Switzerland) · 2022Article
27 more citing papers are in PubMed but not listed here.
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Authors and funding
2 authors.
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Abstract
Based on the virtual bond representation for the nucleotide backbone, we develop a reduced conformational model for RNA. We use the experimentally measured atomic coordinates to model the helices and use the self-avoiding walks in a diamond lattice to model the loop conformations. The atomic coordinates of the helices and the lattice representation for the loops are matched at the loop-helix junction, where steric viability is accounted for. Unlike the previous simplified lattice-based models, the present virtual bond model can account for the atomic details of realistic three-dimensional RNA structures. Based on the model, we develop a statistical mechanical theory for RNA folding energy landscapes and folding thermodynamics. Tests against experiments show that the theory can give much more improved predictions for the native structures, the thermal denaturation curves, and the equilibrium folding/unfolding pathways than the previous models. The application of the model to the P5abc region of Tetrahymena group I ribozyme reveals the misfolded intermediates as well as the native-like intermediates in the equilibrium folding process. Moreover, based on the free energy landscape analysis for each and every loop mutation, the model predicts five lethal mutations that can completely alter the free energy landscape and the folding stability of the molecule.
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