ArticleNucleic acids research2006
A set of nearest neighbor parameters for predicting the enthalpy change of RNA secondary structure formation.
Article in Nucleic acids research, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 76 papers.
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76 citing papers in PubMed.
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- Design of Conditional Guide RNAs for the Logical Regulation of Gene Expression.Methods in molecular biology (Clifton, N.J.) · 2026Article
- SiaRNA: a siamese neural network with bidirectional cross-attention for pairwise siRNA-mRNA efficacy prediction.Frontiers in bioinformatics · 2026Article
- ECSFinder: optimized prediction of evolutionarily conserved RNA secondary structures from genome sequences.Nucleic acids research · 2025Article
- VariantFoldRNA: a flexible, containerized, and scalable pipeline for genome-wide riboSNitch prediction.NAR genomics and bioinformatics · 2025Article
- RNA editing generates mRNA isoforms with distinct stabilities that may expand the thermal tolerance of mRNA and proteins inZoological research · 2025Article
- Using the RNAstructure Software Package to Predict Conserved RNA Structures.Current protocols · 2024Article
- NNDB: An Expanded Database of Nearest Neighbor Parameters for Predicting Stability of Nucleic Acid Secondary Structures.Journal of molecular biology · 2024Article
- START: A Versatile Platform for Bacterial Ligand Sensing with Programmable Performances.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Estimating RNA Secondary Structure Folding Free Energy Changes with efn2.Methods in molecular biology (Clifton, N.J.) · 2024Article
- DeGenPrime provides robust primer design and optimization unlocking the biosphere.Bioinformatics advances · 2024Article
- DNA Structure Design Is Improved Using an Artificially Expanded Alphabet of Base Pairs Including Loop and Mismatch Thermodynamic Parameters.ACS synthetic biology · 2023Article
- Mono-valent salt corrections for RNA secondary structures in the ViennaRNA package.Algorithms for molecular biology : AMB · 2023Article
- RNA Secondary Structure Analysis Using RNAstructure.Current protocols · 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
- High-throughput single-molecule quantification of individual base stacking energies in nucleic acids.Nature communications · 2023Article
- Nearest neighbor rules for RNA helix folding thermodynamics: improved end effects.Nucleic acids research · 2022Article
- Construction and Characterization of a Botrytis Virus F Infectious Clone.Journal of fungi (Basel, Switzerland) · 2022Article
- A Satellite dsRNA Attenuates the Induction of Helper Virus-Mediated Symptoms inFrontiers in microbiology · 2022Article
16 more citing papers are in PubMed but not listed here.
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3 authors.
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Abstract
A complete set of nearest neighbor parameters to predict the enthalpy change of RNA secondary structure formation was derived. These parameters can be used with available free energy nearest neighbor parameters to extend the secondary structure prediction of RNA sequences to temperatures other than 37 degrees C. The parameters were tested by predicting the secondary structures of sequences with known secondary structure that are from organisms with known optimal growth temperatures. Compared with the previous set of enthalpy nearest neighbor parameters, the sensitivity of base pair prediction improved from 65.2 to 68.9% at optimal growth temperatures ranging from 10 to 60 degrees C. Base pair probabilities were predicted with a partition function and the positive predictive value of structure prediction is 90.4% when considering the base pairs in the lowest free energy structure with pairing probability of 0.99 or above. Moreover, a strong correlation is found between the predicted melting temperatures of RNA sequences and the optimal growth temperatures of the host organism. This indicates that organisms that live at higher temperatures have evolved RNA sequences with higher melting temperatures.
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