Rosetta 3.5
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Documentation for RosettaDNA application
Author
Justin Ashworth ashwo.nosp@m.rtj@.nosp@m.uw.ed.nosp@m.u, James Havranek havra.nosp@m.nek@.nosp@m.genet.nosp@m.ics..nosp@m.wustl.nosp@m..edu, Phil Bradley pbrad.nosp@m.ley@.nosp@m.fhcrc.nosp@m..org, Carlos Duarte, David Baker dabak.nosp@m.er@u.nosp@m.w.edu

Metadata

Last updated 2011-02-18. Corresponding authors are Justin Ashworth and David Baker.

Code and Demo

To run the demos (integration tests), obtain the source package, enter directory [rosetta_source]/test/integration/, and run the command line:

./integration.py dna_interface_design

(note: run ./integration.py -h to set additional options and paths that may be necessary depending on your system)

References

New_Library contains code for this purpose

This application provides support for biophysical modeling of protein-DNA interactions. It provides sampling and energetic estimates of structural and mutational degrees of freedom in the protein-DNA interface.

Algorithm

This application is provided to access full-atom, primarily fixed-backbone protocols in the protocols/dna directory through the RosettaScripts and Job Dsitributor schemes. This scheme is highly extensible: this application also provides access to any other class or procedure that is implemented under the RosettaScripts scheme. Currently, the primary difference between this application and the RosettaScripts application is that this one uses a custom JobOutputter class to prepend protein-DNA-specific information to output PDB files.

Limitations

This application is not officially supported for anything that is not described in the referenced literature citations.

Modes

Please see the demos (integration tests) for three example modes for this application. Three modes are provided: automated basepair-specific design, resfile-directed design, and basepair specificity prediction.

Input Files

Required file

Optional

Options

Protocol-Specific Options

Most protocol-specific behavior is specified through the RosettaScripts interface. Here are examples of the primary class options:

General Options

The following general Rosetta command-line options are currently used in demos:

Tips

The demos (integration tests) are designs to run quickly. For higher quality results, additional rotamer sampling can be enabled using the -ex1 and -ex2 command line options. Also, see the scientific tests (mentioned earlier in this documentation under Files) for more useful parameters.

Optimal performance depends upon a few minor modifications of the code and database files. For this reason, alternative database files are provided in test/scientific/cluster/dna_interface_design/rosetta_database_sparse/. The modifications are summarized below:

Expected Outputs

These protocols output files through the JobDistributor scheme. Normally, this results in a PDB file. Often, this PDB file will contain header information that describes the results of the analysis.