title: The determination of RNA folding nearest neighbor parameters.
abstract: The stability of RNA secondary structure can be predicted using a set of nearest neighbor parameters. These parameters are widely used by algorithms that predict secondary structure. This contribution introduces the UV optical melting experiments that are used to determine the folding stability of short RNA strands. It explains how the nearest neighbor parameters are chosen and how the values are fit to the data. A sample nearest neighbor calculation is provided. The contribution concludes with new methods that use the database of sequences with known structures to determine parameter values.
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, WA, USA.
authors.forename: Mirela
authors.initials: M
authors.lastname: Andronescu
authors.forename: Anne
authors.initials: A
authors.lastname: Condon
authors.forename: Douglas H
authors.initials: DH
authors.lastname: Turner
authors.forename: David H
authors.initials: DH
authors.lastname: Mathews
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D059370:RNA Folding; D013816:Thermodynamics
chemical_list: D012313:RNA