ArticleJournal of molecular biology2024
NNDB: An Expanded Database of Nearest Neighbor Parameters for Predicting Stability of Nucleic Acid Secondary Structures.
Article in Journal of molecular biology, 2024. 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.
- Longer Is Not Always Better: Effects of Equilibration Length on Umbrella Sampling Estimations for RNA Hairpin Folding Stabilities.bioRxiv : the preprint server for biology · 2026Article
- Markov models of SHAPE data improve secondary structure prediction.bioRxiv : the preprint server for biology · 2026Article
- Nearest Neighbor Parameters for Estimating RNA Folding Stability withbioRxiv : the preprint server for biology · 2026Article
- Toward Accurate RNA Folding Thermodynamics: Evaluation of Enhanced Sampling Methods for Force Field Benchmarking.Journal of chemical theory and computation · 2026Article
- Nearest Neighbor Parameters for Estimating the Folding Stability of RNA Including Pseudouridine.bioRxiv : the preprint server for biology · 2026Article
- NUPACK: Computational Nucleic Acid Analysis and Design.ACS synthetic biology · 2026Article
- Insights into siRNA Duplex Stability by UV Spectrophotometry Absorbance and Melting Temperature Analyses.ACS omega · 2026Article
- RNA Folding Nearest Neighbor Parameters Including the Modification 1-Methyl-Pseudouridine.bioRxiv : the preprint server for biology · 2026Article
- Deep learning for RNA secondary structure determination: gauging generalizability and broadening the scope of traditional methods.RNA (New York, N.Y.) · 2026Review
- SamplingDesign: RNA design via continuous optimization with coupled variables and Monte-Carlo sampling.Nature communications · 2026Article
- Ubiquitous low-energy RNA fluctuations and energetic coupling measured by chemical probing.bioRxiv : the preprint server for biology · 2026Article
- DMS-informed secondary structure modeling of Epstein-Barr Virus LMP-1 pre-mRNA defines novel elements spanning introns.PloS one · 2026Article
- Deep Learning for RNA Secondary Structure Determination: Gauging Generalizability and Broadening the Scope of Traditional Methods.bioRxiv : the preprint server for biology · 2025Article
- Structural Impact of 3-methylcytosine Modification on the Anticodon Stem-loop of a Neuronally-enriched Arginine tRNA.Journal of molecular biology · 2025Article
- 3D structure and stability prediction of DNA with multi-way junctions in ionic solutions.PLoS computational biology · 2025Article
- AlignmentFold and AlignmentPartition: Improving the align-then-fold approach for RNA secondary structure prediction.bioRxiv : the preprint server for biology · 2025Article
- mRNA folding algorithms for structure and codon optimization.Briefings in bioinformatics · 2025Review
- Alternative splicing in the RBMXL1 5'-UTR induces uORF-mediated translation control in activated B lymphocytes.Scientific reports · 2025Article
- A Multi-Input Neural Network Model for Accurate MicroRNA Target Site Detection.Non-coding RNA · 2025Article
- Robust RNA secondary structure prediction with a mixture of deep learning and physics-based experts.Biology methods & protocols · 2025Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Nearest neighbor thermodynamic parameters are widely used for RNA and DNA secondary structure prediction and to model thermodynamic ensembles of secondary structures. The Nearest Neighbor Database (NNDB) is a freely available web resource (https://rna.urmc.rochester.edu/NNDB) that provides the functional forms, parameter values, and example calculations. The NNDB provides the 1999 and 2004 set of RNA folding nearest neighbor parameters. We expanded the database to include a set of DNA parameters and a set of RNA parameters that includes m
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.