ArticleRNA (New York, N.Y.)2010
On the significance of an RNA tertiary structure prediction.
Article in RNA (New York, N.Y.), 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 67 papers.
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Who cites it
67 citing papers in PubMed.
- Structural Prediction of Coronavirus s2m Kissing Complexes and Extended Duplexes.ACS physical chemistry Au · 2025Article
- Comprehensive Studies on the Regulation of Type 2 Diabetes by Cucurbitane-Type Triterpenoids inPharmaceuticals (Basel, Switzerland) · 2025Article
- Has AlphaFold3 achieved success for RNA?Acta crystallographica. Section D, Structural biology · 2025Article
- Predicting 3D RNA structure from the nucleotide sequence using Euclidean neural networks.Biophysical journal · 2024Article
- State-of-the-RNArt: benchmarking current methods for RNA 3D structure prediction.NAR genomics and bioinformatics · 2024Article
- RNAdvisor: a comprehensive benchmarking tool for the measure and prediction of RNA structural model quality.Briefings in bioinformatics · 2024Article
- Inconsistencies in the Classification of the Family Cydnidae (Hemiptera: Heteroptera: Pentatomoidea) Revealed by Molecular Apomorphies in the Secondary and Tertiary Structures of 18S rRNA Length-Variable Region L (LVR L).International journal of molecular sciences · 2024Article
- RNA 3D structure modeling by fragment assembly with small-angle X-ray scattering restraints.Bioinformatics (Oxford, England) · 2023Article
- RNA Secondary Structure Analysis Using RNAstructure.Current protocols · 2023Article
- Molecular Apomorphies in the Secondary and Tertiary Structures of Length-Variable Regions (LVRs) of 18S rRNA Shed Light on the Systematic Position of the Family Thaumastellidae (Hemiptera: Heteroptera: Pentatomoidea).International journal of molecular sciences · 2023Article
- Predicting 3D structures and stabilities for complex RNA pseudoknots in ion solutions.Biophysical journal · 2023Article
- Article
- RNA 3D Structure Comparison Using RNA-Puzzles Toolkit.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Computational Pipeline for Reference-Free Comparative Analysis of RNA 3D Structures Applied to SARS-CoV-2 UTR Models.International journal of molecular sciences · 2022Article
- LTPConstraint: a transfer learning based end-to-end method for RNA secondary structure prediction.BMC bioinformatics · 2022Article
- A Comprehensive Computational Investigation into the Conserved Virulent Proteins ofMolecules (Basel, Switzerland) · 2022Article
- RNAStat: An Integrated Tool for Statistical Analysis of RNA 3D Structures.Frontiers in bioinformatics · 2021Article
- Salt-Dependent RNA Pseudoknot Stability: Effect of Spatial Confinement.Frontiers in molecular biosciences · 2021Article
- Identification and characterization of hippuristanol-resistant mutants reveals eIF4A1 dependencies within mRNA 5' leader regions.Nucleic acids research · 2020Article
- RNA-Puzzles toolkit: a computational resource of RNA 3D structure benchmark datasets, structure manipulation, and evaluation tools.Nucleic acids research · 2020Article
7 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors.
Funding
Abstract
Tertiary structure prediction is important for understanding structure-function relationships for RNAs whose structures are unknown and for characterizing RNA states recalcitrant to direct analysis. However, it is unknown what root-mean-square deviation (RMSD) corresponds to a statistically significant RNA tertiary structure prediction. We use discrete molecular dynamics to generate RNA-like folds for structures up to 161 nucleotides (nt) that have complex tertiary interactions and then determine the RMSD distribution between these decoys. These distributions are Gaussian-like. The mean RMSD increases with RNA length and is smaller if secondary structure constraints are imposed while generating decoys. The compactness of RNA molecules with true tertiary folds is intermediate between closely packed spheres and a freely jointed chain. We use this scaling relationship to define an expression relating RMSD with the confidence that a structure prediction is better than that expected by chance. This is the prediction significance, and corresponds to a P-value. For a 100-nt RNA, the RMSD of predicted structures should be within 25 A of the accepted structure to reach the P <or= 0.01 level if the secondary structure is predicted de novo and within 14 A if secondary structure information is used as a constraint. This significance approach should be useful for evaluating diverse RNA structure prediction and molecular modeling algorithms.
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