NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure
Open accessAbstract
The Nearest Neighbor Database (NNDB, http://rna.urmc.rochester.edu/NNDB) is a web-based resource for disseminating parameter sets for predicting nucleic acid secondary structure stabilities. For each set of parameters, the database includes the set of rules with descriptive text, sequence-dependent parameters in plain text and html, literature references to experiments and usage tutorials. The initial release covers parameters for predicting RNA folding free energy and enthalpy changes.
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The QUBO formulation includes free energy e_qi derived from empirical thermodynamic data.
“Each quartet variable q i is assigned a free energy e q i derived from empirical thermodynamic data, as described in Ref. [48]”
From Towards secondary structure prediction of longer mRNA sequences using a quantum-centric optimization scheme (2025) · cites this paper as [48]
The Introduction says the free-energy parameters are based on empirical rules generally derived from optical melting experiments, and Website Organization describes parameter values for structural features. The paper does not describe QUBO quartet variables or assigning an energy e_qi to each one, so it supports the empirical basis of the energies but not that specific formulation. (LLM, conf=0.84)
Experimental — accuracy not yet measuredG:U wobble pairing contributes strongly to the energetic stability of a folded RNA sequence but only weakly, if at all, to the stability of its reverse complement.
“Unlike Watson-Crick base pairs, wobble pairs contribute highly to the energetic stability of the folded structure of their sequence, but only slightly, if at all, to the stability of the folded reverse complement.”
From The paradox of dual roles in the RNA world: resolving the conflict between stable folding and templating ability (2013) · cites this paper as Turner and Mathews 2010
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“[48].”
- Authors
- Turner, D. H., & Mathews, D. H.
- Affiliations
- University of Rochester Medicine (US)
- Corresponding author
- Mathews, David H.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2009-10-30
- Volume
- 38
- Issue
- suppl_1
- Pages
- D280-D282
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC2808915
- OpenAlex
- W2159117141
- Cited by
- 575
- References
- 20
- Citations by year
- 2026: 32 · 2025: 36 · 2024: 41 · 2023: 53 · 2022: 55 · 2021: 32 · 2020: 41 · 2019: 37 · 2018: 39 · 2017: 41 · 2016: 29 · 2015: 38 · 2014: 27 · 2013: 27 · 2012: 26
- FWCI
- 6.17
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Nucleic Acids Research (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- HighWire Press Open Archive (submittedVersion)
- Funders
- National Institutes of Health
- National Institute of General Medical Sciences (GM 22939, R01GM022939, R01GM076485, GM076485)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Keywords
- nucleic acid secondary structure, RNA folding, free energy prediction, enthalpy prediction, online databases
- MeSH terms
- Algorithms, Base Sequence, Molecular Sequence Data, Nucleic Acid Conformation, Nucleic Acid Denaturation, RNA, Software, Thermodynamics, Information Storage and Retrieval, Computational Biology, Internet, Databases, Genetic, Databases, Nucleic Acid
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