iFoldRNA v2: folding RNA with constraints

Bioinformatics. 2015 Sep 1;31(17):2891-3. doi: 10.1093/bioinformatics/btv221. Epub 2015 Apr 24.


A key to understanding RNA function is to uncover its complex 3D structure. Experimental methods used for determining RNA 3D structures are technologically challenging and laborious, which makes the development of computational prediction methods of substantial interest. Previously, we developed the iFoldRNA server that allows accurate prediction of short (<50 nt) tertiary RNA structures starting from primary sequences. Here, we present a new version of the iFoldRNA server that permits the prediction of tertiary structure of RNAs as long as a few hundred nucleotides. This substantial increase in the server capacity is achieved by utilization of experimental information such as base-pairing and hydroxyl-radical probing. We demonstrate a significant benefit provided by integration of experimental data and computational methods.

Availability and implementation: http://ifoldrna.dokhlab.org

Contact: dokh@unc.eu.

Publication types

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

MeSH terms

  • Algorithms*
  • Base Pairing*
  • Computational Biology / methods*
  • Computer Simulation
  • Hydroxyl Radical / chemistry*
  • Models, Molecular
  • Nucleic Acid Conformation
  • RNA / chemistry*
  • RNA / genetics
  • Sequence Analysis, RNA / methods*
  • Software*


  • Hydroxyl Radical
  • RNA