Secondary Structure Prediction of Single Sequences Using RNAstructure

Methods Mol Biol. 2016;1490:15-34. doi: 10.1007/978-1-4939-6433-8_2.


RNA secondary structure is often predicted using folding thermodynamics. RNAstructure is a software package that includes structure prediction by free energy minimization, prediction of base pairing probabilities, prediction of structures composed of highly probably base pairs, and prediction of structures with pseudoknots. A user-friendly graphical user interface is provided, and this interface works on Windows, Apple OS X, and Linux. This chapter provides protocols for using RNAstructure for structure prediction.

Keywords: RNA folding thermodynamics; RNA statistical mechanics; RNA structure prediction.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Models, Molecular
  • Models, Statistical
  • Nucleic Acid Conformation*
  • Nucleotide Motifs
  • RNA / chemistry*
  • RNA Folding*
  • Software*
  • Thermodynamics
  • User-Computer Interface
  • Web Browser


  • RNA