External Resources

Resources for oxDNA

Here we provide a list of publicly available external resources that have been developed to help use oxDNA

• The oxDNA and oxDNA2 models have been implemented in LAMMPS in the USER-CGDNA package. This was developed by Oliver Henrich (with the help of Tom E. Ouldridge, F. Romano and L. Rovigatti). The package documentation can be found here. The code comes with any regular download from the central LAMMPS repository, and it is also available here.

• The tacoxDNA suite of tools allows the conversion of configurations to and from the oxDNA format. These can be used at the tacoxDNA webserver and the underlying python codes are available here.

• webDNA: a web front-end for oxDNA produced by the group of Matthew Patitz at University of Arkansa is available here

• oxView: a browser-based viewer from the Šulc group is available here. It is specifically designed for oxDNA, and allows manipulation as well as viewing of structures.

• The Šulc group's oxDNA analysis tools: https://github.com/sulcgroup/oxdna_analysis_tools

or produce output in oxDNA format

• multi-resolution DNA (mrDNA). This programme from the Aksimentiev group can simulate DNA nanostructures at multiple coarser levels of detail than oxDNA. It can output in oxDNA format. A tutorial can be found here and the repository for the code here.

• Adenita A preprint introducing this design tool is available from bioRxiv.

If you have any resources that you want added do let us know.

Other DNA nanotechnology modelling tools

• CanDo
• Aksimentiev group tools

DNA nanotechnology design tools

• cadnano
• Tiamat
• vHelix
• Wireframe DNA origami tools from the Bathe group
• Adenita