1. NNDB: An Expanded Database of Nearest Neighbor Parameters for Predicting Stability of Nucleic Acid Secondary Structures.
- Author
-
Mittal A, Turner DH, and Mathews DH
- Subjects
- Thermodynamics, Databases, Nucleic Acid, Computational Biology methods, Nucleic Acid Conformation, RNA chemistry, DNA chemistry
- 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
6 A in addition to the canonical RNA nucleobases. The site was redesigned using the Quarto open-source publishing system. A downloadable PDF version of the complete resource and downloadable sets of nearest neighbor parameters are available., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)- Published
- 2024
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