RNA Secondary Structure Prediction

Curr Protoc Nucleic Acid Chem. 2016 Dec 1;67:11.2.1-11.2.19. doi: 10.1002/cpnc.19.


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.

Keywords: RNA folding; RNA secondary structure prediction; binding affinity; free energy minimization; partition function; thermodynamics.

MeSH terms

  • Base Pairing
  • Nucleic Acid Conformation*
  • Probability
  • RNA / chemistry*


  • RNA