ArticleJournal of molecular biology2011
Statistical potentials for hairpin and internal loops improve the accuracy of the predicted RNA structure.
Article in Journal of molecular biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- RNAStat: An Integrated Tool for Statistical Analysis of RNA 3D Structures.Frontiers in bioinformatics · 2021Article
- Modeling Loop Composition and Ion Concentration Effects in RNA Hairpin Folding Stability.Biophysical journal · 2020Article
- The Coevolution of Fungal Mitochondrial Introns and Their Homing Endonucleases (GIY-YIG and LAGLIDADG).Genome biology and evolution · 2020Article
- How to benchmark RNA secondary structure prediction accuracy.Methods (San Diego, Calif.) · 2019Review
- bpRNA: large-scale automated annotation and analysis of RNA secondary structure.Nucleic acids research · 2018Article
- Network Theory Tools for RNA Modeling.WSEAS transactions on mathematics · 2013Article
- Visualizing RNA base-pairing probabilities with RNAbow diagrams.RNA (New York, N.Y.) · 2013Article
- You tell Carl that some of my best friends are Eukaryotes: Carl R. Woese (1928-2012).RNA (New York, N.Y.) · 2013Article
- CompaRNA: a server for continuous benchmarking of automated methods for RNA secondary structure prediction.Nucleic acids research · 2013Article
- Unconventional translation of C9ORF72 GGGGCC expansion generates insoluble polypeptides specific to c9FTD/ALS.Neuron · 2013Article
- Two accurate sequence, structure, and phylogenetic template-based RNA alignment systems.BMC systems biology · 2013Article
- rCAD: A Novel Database Schema for the Comparative Analysis of RNA.Proceedings ... IEEE International Conference on eScience. IEEE International Conference on eScience · 2011Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
RNA is directly associated with a growing number of functions within the cell. The accurate prediction of different RNA higher-order structures from their nucleic acid sequences will provide insight into their functions and molecular mechanics. We have been determining statistical potentials for a collection of structural elements that is larger than the number of structural elements determined with experimentally determined energy values. The experimentally derived free energies and the statistical potentials for canonical base-pair stacks are analogous, demonstrating that statistical potentials derived from comparative data can be used as an alternative energetic parameter. A new computational infrastructure-RNA Comparative Analysis Database (rCAD)-that utilizes a relational database was developed to manipulate and analyze very large sequence alignments and secondary-structure data sets. Using rCAD, we determined a richer set of energetic parameters for RNA fundamental structural elements including hairpin and internal loops. A new version of RNAfold was developed to utilize these statistical potentials. Overall, these new statistical potentials for hairpin and internal loops integrated into the new version of RNAfold demonstrated significant improvements in the prediction accuracy of RNA secondary structure.
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