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rna_predict

The rna_predict Python package models a complete workflow for RNA tertiary structure prediction using the secondary structure information as well as optional, additional constraints.

The modelling is done using Rosetta and its rna_denovo protocol.

Additional constraints, for example from co-evolutional anaylsis, can be included to improve the prediction quality.

A utility to convert residue-residue contacts into atom-atom constraints is included.

rna_predict also comes with tools to cluster and visualize the prediction results and to compare them to a native crystal strcture, if available.

Installation and Configuaration

The rna_predict Python package has the following dependencies:

  • biopython
  • matplotlib
  • numpy

To install the package (and the dependencies, if necessary), run:

python setup.py install

Additionally, rna_predict depends on Rosetta. However, a few minor modifications to the Rosetta source are required. For a detailed Rosetta compilation and installation guide see doc/rosetta.rst or the HTML documentation.

A few configuration options can be overridden in ~/.rna_predict/sysconfig. For details refer to the documentation.

Usage

rna_predict comes with a command line interface. To see all available options run:

rna_predict --help

For detailed usage information refer to the documentation.

Documentation

The HTML documentation can be found here.

A PDF version can be downloaded from here.

If you downloaded a source package or checked out the source from Git, you can also build the HTML documentation yourself. For that, rna_predict needs to be installed as well as the Sphinx Python package.

To build the docs run:

python setup.py build_sphinx

After that, the HTML output can be found in build/sphinx/html.

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Python package for RNA tertiary structure prediction

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