Experiment-Assisted Secondary Structure Prediction with RNAstructure

Methods Mol Biol. 2016;1490:163-76. doi: 10.1007/978-1-4939-6433-8_10.


Experimental probing data can be used to improve the accuracy of RNA secondary structure prediction. The software package RNAstructure can take advantage of enzymatic cleavage data, FMN cleavage data, traditional chemical modification reactivity data, and SHAPE reactivity data for secondary structure modeling. This chapter provides protocols for using experimental probing data with RNAstructure to restrain or constrain RNA secondary structure prediction.

Keywords: Chemical modification data; RNA structure prediction; SHAPE; Thermodynamics.

Publication types

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

MeSH terms

  • Nucleic Acid Conformation*
  • RNA / chemistry*
  • Software*
  • Thermodynamics
  • User-Computer Interface
  • Web Browser


  • RNA