Secondary Structure


Online Submission

AMU Homepage

Download ModeRNA

ModeRNA is intellectual property of Magdalena Rother, Kristian Rother, Tomasz Puton, and Janusz Bujnicki (c) 2009 Available under the conditions of the General Public License.

Download source code

This provides you with the entire ModeRNA program as pure Python, that runs on both Windows and UNIX.

Moderna Version 1.7.1 (source) - 13 MB - tar.gz archive,

Moderna Version 1.7.1 (source) - 13 MB - zip archive

Download Windows binary

This gives you a standalone version of ModeRNA created with the py2exe program.

Moderna Version 1.7.0 (.exe) - 23 MB,

RNA Secondary Structures

To facilitate finding a good template, we have extracted sequences and secondary structures for some representative sets of RNA PDB structures.

Structures occuring in the rnaDB2005 (from Jane Richardsons lab) used to generate the ModeRNA fragment library. [download]
Representative structures collected from DARTS. [download]
High-resolution x-ray structures (<=2.0A). [download]
Set of 99 tRNA chains used to benchmark ModeRNA. [download]

Larger Linker Libraries

To allow insertion of larger linkers, you can use one of the libraries below. They have not been included in the main distribution for their size. To use a library, download it and replace the file data/LIR_fragments.lib .

Linkers up to 100nt length (111MB). [download]

Example files for modeling the Group I Intron

The files here have been used to build a model of the Azoarcus Group I Intron. For details, see the Group I Intron page.

[ 1Y0Q template PDB structure ]
[ alignment (FASTA) ]
[ excerpt from 1GID to model tertiary interaction sites ]
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