title: RNA Secondary Structure Prediction.
abstract: In this unit, protocols are provided for predicting RNA secondary structure with the user-friendly RNAstructure desktop computer program and the RNAstructure Web server. The minimum free energy structure and a set of suboptimal structures with similar free energies are predicted. Prediction of high-affinity oligonucleotide binding sites to a structured RNA target is also presented. © 2016 by John Wiley & Sons, Inc.
authors.affiliation: University of Rochester, Rochester, New York.
authors.forename: David H
authors.initials: DH
authors.lastname: Mathews
authors.affiliation: University of Rochester, Rochester, New York.
authors.forename: Douglas H
authors.initials: DH
authors.lastname: Turner
authors.affiliation: University of Rochester, Rochester, New York.
authors.forename: Richard M
authors.initials: RM
authors.lastname: Watson
mesh_terms: D020029:Base Pairing; D009690:Nucleic Acid Conformation; D011336:Probability; D012313:RNA / Q000737:chemistry*
chemical_list: D012313:RNA
keywords: RNA folding; RNA secondary structure prediction; binding affinity; free energy minimization; partition function; thermodynamics