ArticleNucleic acids research2017
A sensitivity analysis of RNA folding nearest neighbor parameters identifies a subset of free energy parameters with the greatest impact on RNA secondary structure prediction.
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 21 papers.
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Who cites it
21 citing papers in PubMed.
- RNA motifs, RNA structure, and motif context analyzed by RNAanalyzer3.Nucleic acids research · 2026Article
- Nearest Neighbor Parameters for Estimating the Folding Stability of RNA Including Pseudouridine.bioRxiv : the preprint server for biology · 2026Article
- RNA Folding Nearest Neighbor Parameters Including the Modification 1-Methyl-Pseudouridine.bioRxiv : the preprint server for biology · 2026Article
- Hierarchical analysis of RNA secondary structures with pseudoknots based on sections.PLoS computational biology · 2026Article
- SparseRNAfolD: optimized sparse RNA pseudoknot-free folding with dangle consideration.Algorithms for molecular biology : AMB · 2024Article
- Estimating RNA Secondary Structure Folding Free Energy Changes with efn2.Methods in molecular biology (Clifton, N.J.) · 2024Article
- DNA Structure Design Is Improved Using an Artificially Expanded Alphabet of Base Pairs Including Loop and Mismatch Thermodynamic Parameters.ACS synthetic biology · 2023Article
- DNA Structure Design Is Improved Using an Artificially Expanded Alphabet of Base Pairs Including Loop and Mismatch Thermodynamic Parameters.bioRxiv : the preprint server for biology · 2023Article
- A Test and Refinement of Folding Free Energy Nearest Neighbor Parameters for RNA Including NJournal of molecular biology · 2022Article
- Secondary structure prediction for RNA sequences including NNature communications · 2022Article
- Vfold2D-MC: A Physics-Based Hybrid Model for Predicting RNA Secondary Structure Folding.The journal of physical chemistry. B · 2021Article
- LinearPartition: linear-time approximation of RNA folding partition function and base-pairing probabilities.Bioinformatics (Oxford, England) · 2020Article
- Determining parameters for non-linear models of multi-loop free energy change.Bioinformatics (Oxford, England) · 2019Article
- Estimating uncertainty in predicted folding free energy changes of RNA secondary structures.RNA (New York, N.Y.) · 2019Article
- How to benchmark RNA secondary structure prediction accuracy.Methods (San Diego, Calif.) · 2019Review
- Validation of the nearest-neighbor model for Watson-Crick self-complementary DNA duplexes in molecular crowding condition.Nucleic acids research · 2019Article
- Chemically Accurate Relative Folding Stability of RNA Hairpins from Molecular Simulations.Journal of chemical theory and computation · 2018Article
- Challenges and approaches to predicting RNA with multiple functional structures.RNA (New York, N.Y.) · 2018Review
- Analysis of RNA nearest neighbor parameters reveals interdependencies and quantifies the uncertainty in RNA secondary structure prediction.RNA (New York, N.Y.) · 2018Article
- PATTERNA: transcriptome-wide search for functional RNA elements via structural data signatures.Genome biology · 2018Article
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5 authors.
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Abstract
Nearest neighbor parameters for estimating the folding energy changes of RNA secondary structures are used in structure prediction and analysis. Despite their widespread application, a comprehensive analysis of the impact of each parameter on the precision of calculations had not been conducted. To identify the parameters with greatest impact, a sensitivity analysis was performed on the 291 parameters that compose the 2004 version of the free energy nearest neighbor rules. Perturbed parameter sets were generated by perturbing each parameter independently. Then the effect of each individual parameter change on predicted base-pair probabilities and secondary structures as compared to the standard parameter set was observed for a set of sequences including structured ncRNA, mRNA and randomized sequences. The results identify for the first time the parameters with the greatest impact on secondary structure prediction, and the subset which should be prioritized for further study in order to improve the precision of structure prediction. In particular, bulge loop initiation, multibranch loop initiation, AU/GU internal loop closure and AU/GU helix end parameters were particularly important. An analysis of parameter usage during folding free energy calculations of stochastic samples of secondary structures revealed a correlation between parameter usage and impact on structure prediction precision.
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