NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure

Nucleic Acids Res. 2010 Jan;38(Database issue):D280-2. doi: 10.1093/nar/gkp892. Epub 2009 Oct 30.


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.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Algorithms
  • Base Sequence
  • Computational Biology / methods*
  • Computational Biology / trends
  • Databases, Genetic*
  • Databases, Nucleic Acid*
  • Information Storage and Retrieval / methods
  • Internet
  • Molecular Sequence Data
  • Nucleic Acid Conformation*
  • Nucleic Acid Denaturation
  • RNA / chemistry*
  • Software
  • Thermodynamics


  • RNA