Welcome to iFoldRNA Ver 2.0 - a web portal for interactive RNA folding simulations. We perform discrete molecular dynamics simulations of RNA using coarse-grained structural models (three-beads/residue).

Important note: Please visit the Help Center before submitting your RNA foldig jobs. Especially, please read the section of "Choosing iFoldRNA simulation-time" for the appropraite simulation time.

To cite iFoldRNA in your research, please use the following references:

  • A. Krokhotin, K. Houlihan, and N. V. Dokholyan, "iFoldRNA v2: folding RNA with constraints" Bioinformatics, 31: 2891-2893 (2015).
    [Adobe PDF]
  • S. Sharma, F. Ding, and N. V. Dokholyan, "iFoldRNA:Three-dimensional RNA structure prediction and folding" Bioinformatics, 24: 1951-1952 (2008).
    [Adobe PDF] [Supporting Information, Adobe PDF]
  • F. Ding, S. Sharma, P. Chalasani, V. V. Demidov, N. E. Broude, and N. V. Dokholyan, "Large scale simulations of 3D RNA folding by discrete molecular dynamics: From structure prediction to folding mechanisms" RNA, 14: 1164-1173 (2008).
    [Adobe PDF] [Supporting Information, Adobe PDF]

We recommend you to carefully read the Terms of Use and the Privacy Policy. If you have any questions, please contact the iFold team via email (delete spaces): iFoldRNA @ listserv.unc.edu

How good is your RNA model? Submit the following form to estimate significance of RNA structure prediction

Length of the RNA molecule :
Predicted RMSD :
You may now download the source code for this tool here.