Stepwise

Stepwise is a Rosetta application for generating highly accurate de novo 3D models of small RNA and protein motifs. It can be used for both structure prediction and design.

Installation

To run Stepwise, Rosetta must be installed:

• Request a license and download the software at rosettacommons.

• See the Rosetta installation documentation at rosettacommons.

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

stepwise -fasta my_rna_sequence.fasta -s start_helix.pdb  -out:file:silent swm_rebuild.out

Documentation

• Documentation is available at: rosettacommons.

License

Copyright © of Stepwise Source Code is described in license-and-download.

References

Stepwise monte carlo is unpublished as of May 2016. References for the stepwise assembly method:

Das, R. (2013)
Atomic-accuracy prediction of protein loop structures enabled by an RNA-inspired ansatz
PLoS ONE 8 (10): e74830. | Paper | Link

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

Related Packages

• RNAdesign
• RNA de novo
• ERRASER
• RNAMake
• RiboVis

Developed by Rosetta Commons.

README by Kalli Kappel, May 2016.