articleNucleic Acids ResearchOct 30, 2009GOLD OA

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

DHDouglas H. TurnerDHDavid H. Mathews

University of Rochester Medical Center

PubMed
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Abstract

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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Topics & keywords

Topics
Keywords
  • Biology
  • Protein secondary structure
  • k-nearest neighbors algorithm
  • Nucleic acid
  • Set (abstract data type)
  • Stability (learning theory)
  • Folding (DSP implementation)
  • RNA
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