ModeRNA - Comparative Modeling of RNA Structures
Secondary Structure


Online Submission

AMU Homepage


A program for comparative RNA modeling

by Magdalena Rother, Kristian Rother, Tomasz Puton, Janusz Bujnicki

(c) 2009 Available under the conditions of the GPL License.

What is ModeRNA

ModeRNA is a program for comparative modeling of RNA 3D structures. It requires a pairwise sequence alignment and a structural template to generate a 3D structural model of the target RNA sequence via either a fully automated or script-based approaches. ModeRNA is capable of handling 115 different nucleotide modifications and bridging gaps using fragments derived from an extensive fragment library.

Apart from that, ModeRNA offers a multitude of functions to examine and modify RNA structure files. ModeRNA can be integrated into other programs via Python scripting.

If you wish to learn the basics of ModeRNA, we recommend that you read the Tutorial and/or the Frequently Asked Questions.


  • 2011/09/12 - Bug with Biopython 1.58 fixed.
  • 2011/05/18 - Online submission is available at:
  • 2011/05/18 - ModeRNA 1.7.0 released with command for stacking calculation (RELEASE NOTES).
  • 2010/11/19 - ModeRNA 1.6.0 released with command for directly changing sequence.
  • 2010/11/10 - Updated command reference.
  • 2010/10/12 - New structure editing tutorial.
  • 2010/10/09 - ModeRNA 1.5.2 released with validation of command parameters.
  • 2010/07/21 - ModeRNA 1.5.1 released with better nucleotide recognition.
  • 2010/07/21 - ModeRNA 1.5 released with secondary structure modeling functions.
  • 2010/02/13 - ModeRNA 1.4 released with easier installation & cleanup feature.
  • 2010/02/13 - ModeRNA 1.3 released with improved linker/backbone modeling.
  • 2009/11/23 - ModeRNA 1.2 released with changed order of sequences in the alignment.
  • 2009/09/21 - ModeRNA 1.1 released with many improvements and bugfixes.

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