The ROAD software package automates the design of RNA nanostructures using the RNA origami method and consists of the following main programs:
- RNAbuild - generates 3D PDB coordinate files from a blueprint .
- Revolvr - repeatedly mutates a randomized RNA starting sequence until it folds into a target 2D structure under the ViennaRNA folding model.
- Batch_revolvr - runs Revolvr multiple times to create different candidate designs for the same blueprint.
- RNAvis - analyzes and animates one potential folding path from a blueprint.
- flip_trace - outputs a blueprint in all four possible orientations.
- trace_analysis - parses a blueprint and outputs analyses and helpful variants of the blueprint.
- trace_pattern - parses a blueprint and outputs the dot-paren notation for the structure in the blueprint, as well as the sequence constraints. It creates an input for Revolvr.
- trace - threads a sequence onto a blueprint. Only used by Revolvr.
When using this software in publications please cite:
To run RNAbuild you will need to first install a Perl environment. Next, to run Revolvr, you will additionally need to install the ViennaRNA package. Finally, you will need a plaintext editor that can copy/paste blocks of fixed-width text (using so-called “block” or “column” mode) such as TextEdit on MacOS, or Notepad++ and Vim on Windows.
This software was written and tested with Perl v5.18.2 for MacOS, and ViennaRNA versions 2.1.9 and 2.4.10. Installation for Perl and ViennaRNA should be a few minutes. Software was tested on a Mid 2012 Macbook Pro running El Capitan 10.11.6 and a Mid 2015 Macbook Pro running Sierra 10.12.6.
