RNA Design for Fixed-Backbone Optimization
RNAdesign is a Rosetta application for redesigning the sequence of a given RNA structure. This method can be used to predict the primary sequence preferences of RNA structures and suggest mutations to stabilize a particular 3D motif.
There is a server for this application at RNA Redesign.
Alternatively, rna_design is available as part of Rosetta. To download and install Rosetta:
Request a license and download the software at rosettacommons.
See the Rosetta installation documentation at rosettacommons.
Once Rosetta is installed, RNAdesign can be run from the command line, e.g.:
rna_design -s chunk001_uucg_RNA.pdb -nstruct 3 -ex1:level 4 -dump -score:weights farna/rna_hires.wts
Documentation is available at: rosettacommons.
Documentation for the server can be found at RNA Redesign.
Copyright © of RNAdesign Source Code is described in license-and-download.
Yesselman, J.D., and Das, R. (2015)
RNA-Redesign: A web server for fixed-backbone 3D design of RNA
Nucleic Acid Research 43 (W1): W498 - W501. | Paper | Link | Server
Das, R., Karanicolas, J., and Baker, D. (2010)
Atomic accuracy in predicting and designing noncanonical RNA structure
Nature Methods 7: 291 - 294. | Paper | Link
Developed by Rosetta Commons.
README by Kalli Kappel, May 2016.
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