RNA de novo

RNA de novo is a Rosetta application for making 3D models of RNA using the Fragment Assembly of RNA with Full Atom Refinement (FARFAR) method.

Installation

To run RNA de novo, Rosetta must be installed:

• Request a license and download the software at rosettacommons.

• See the Rosetta installation documentation at rosettacommons.

• Once Rosetta is installed, rna_denovo can be run from the command line, e.g.:

rna_denovo -fasta my_rna_sequence.fasta -nstruct 100 -minimize_rna -out::file::silent my_rna_structures.out

• The helper script rna_denovo_setup.py, also found within Rosetta, may be useful in setting up rna_denovo runs, see documentation at rosettacommons.

Documentation

• Documentation is available at: rosettacommons.

License

Copyright © of RNA de novo Source Code is described in license-and-download.

References

Sripakdeevong, P., Kladwang, W., and Das, R. (2011)
An enumerative stepwise ansatz enables atomic-accuracy RNA loop modeling
Proceedings of the National Academy of Sciences U.S.A. 108 (51): 20573 - 20578. | Paper | Link

Das, R., Karanicolas, J., and Baker, D. (2010)
Atomic accuracy in predicting and designing noncanonical RNA structure
Nature Methods 7: 291 - 294. | Paper | Link

Das, R. and Baker, D. (2007)
Automated de novo prediction of native-like RNA tertiary structures
Proceedings of the National Academy of Sciences U.S.A. 104 (37): 14664 - 14669. | Paper | Link

Das, R., Kudaravalli, M., Jonikas, M., Laederach, A., Fong, R., Schwans, J.P., Baker, D., Piccirilli, J.A., Altman, R.B., and Herschlag, D. (2008)
Structural inference of native and partially folded RNA by high throughput contact mapping
Proceedings of the National Academy of Sciences U.S.A. 105 (11): 4144 - 4149. | Paper | Link

Related Packages

• Stepwise
• RNAdesign
• ERRASER
• RNAMake
• RiboVis

Workflows

• I think my RNA has a 3D structure

Developed by Rosetta Commons.

README by Kalli Kappel, May 2016.