Predicting RNA-RNA Interactions Using RNAstructure

Methods Mol Biol. 2016;1490:51-62. doi: 10.1007/978-1-4939-6433-8_4.


RNA-RNA binding is a required step for many regulatory and catalytic processes in the cell. Identifying RNA-RNA hybridization sites is challenging because of the competition between intramolecular and intermolecular structure formation. A complete picture of RNA-RNA binding includes an understanding of single-stranded folding and binding site accessibility, and is strongly concentration-dependent. This chapter provides guidance for using RNAstructure to predict RNA-RNA binding sites and RNA-RNA structures, utilizing free energy minimization and partition function calculations. RNAstructure is freely available at .

Keywords: Bimolecular RNA structure; RNA Duplex Formation; RNA hybridization.

Publication types

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

MeSH terms

  • Algorithms
  • Base Pairing*
  • Computational Biology / methods
  • Nucleic Acid Conformation*
  • RNA / chemistry*
  • RNA / genetics
  • RNA Folding*
  • Software*
  • User-Computer Interface
  • Web Browser


  • RNA