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
- 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