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Software tools

As part of our research efforts, we develop tools for computer simulation, analysis and visualization. Most of the tools that we develop can be found on our github account.


We codevelop oxDNA simulation package. The package is hosted on sourceforge repository, and documentation is provided on


An extension of oxDNA/oxRNA models that also allows you to represent proteins. It can be downloaded here, for examples of use check this tutorial.

oxDNA/oxRNA simulation analysis

A new set of Python tools for automated analysis of large nanostructure simulations. The scripts with documentation and examples are provided here.

A new tool for interactive visualization, editing and analysis of DNA and RNA nanostructures. Very fast, user-friendly and platform independent. Runs in any web-browser with JavaScript support. Check it out!

Online services

A new server for simulation analysis and simulations of nucleic acid nanostructures. It is equipped with 8 NVIDIA RTX 2080Ti GPUs and free to use.

A repository server for deposition of DNA, RNA and protein-DNA hybrid nanostructure designs, with the incentive to provide a resouce where all nanostructures can be shared in a common format.


Most of our tools are fully documented on our github account. Also check out oxDNA tutorial youtube channel.


Nano Building Game:

An outreach game designed to illustrate principles of designed systems for self-assembly