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ModeRNA server

A server for RNA structure modeling and analysis

by Magdalena Rother, Kaja Milanowska, Tomasz Puton, Kristian Rother, and Janusz M. Bujnicki.

http://iimcb.genesilico.pl/modernaserver/

What is the ModeRNA server?

This service is based on the ModeRNA software for RNA 3D structure prediction, analysis, and manipulation.

Currently, the server allows you to:

  • build a model (requires a pairwise sequence alignment and a structural template).
  • find template (looks for potential templates using ParAlign and Rfam).
  • align sequences (prepares an alignment between two RNA sequences using R-coffee).
  • convert PDB naming (changes nomenclature in a PDB file).
  • clean up a structure (remove water, ions, and ligands, adds missing P atoms and changes '*' into ''' in ribose).
  • remove modifications (replace modified nucleotides with standard ones).
  • get a sequence (returns the sequence obtained from atomic coordinates in one-letter-code).
  • get a secondary structure (extract the 2D structure from 3D and returns it in the Vienna format).
  • analyze geometry (checks whether the residues of a structure have any unusual features like strange bond and angle values).

To execute your request go to the [submit] section.


The server was tested on the following browsers:
  • Windows: Internet Explorer v. 8 or higher, Firefox v. 4, Google Chrome, Safari 5, Opera v. 10 or higher
  • Linux: Firefox v. 4, Google Chrome, Opera v. 10 or higher
  • Mac OS: Firefox v. 4, Google Chrome, Safari 5, Opera v. 10 or higher
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