Nanobase is a respository of DNA/RNA and protein nanostructures. It is a public resource for the bionanotechnology community to share and reuse their computational and experimental designs, with the goal of becoming RCSB PDB-like database and encouraging more collaboration and reusability of designs developed in our community.
Find the repository at https://nanobase.org/.
OxDNA.org is a cloud-based platform to run oxdna simulations. Their goal is to facilitate development of more advanced and complex designs in the fields of DNA and RNA nanotechnology by facilitating non-experts to run simple simulations. The simulations this server supports are equilibrium sampling of assembled designs, meant to assist users to test in silico their designs before taking them to the lab.
Find more information at https://oxdna.org/.
tacoxDNA (Tools and Converters for oxDNA) is a collection of tools initially developed to help oxDNA users. It was developed by Dr. Lorenzo Rovigatti, used for seamless conversion between multiple file-types, including:
Find more information at https://github.com/lorenzo-rovigatti/tacoxDNA.
PPView is a browser-based javascript app for visualizing patchy particle systems. It was developed by Dr. Michael Matthies at Arizona State University and Technical University of Munich.
Find more information at https://github.com/zoombya/ppview.
Access the tool at https://zoombya.github.io/ppview/.
cogli2 is a simple program for visualizing trajectories of course-grained simulations such as oxDNA or patchy particles. It was developed by Dr. Lorenzo Rovigatti at Sapienza University of Rome.
Find more information at https://sourceforge.net/projects/cogli1/.