Adenita

Publisher: Elisa de Llano

Updated: June 28, 2022


Latest versions

Windows: 0.13.0 on SAMSON 4.0.0

Linux: 0.13.0 on SAMSON 4.0.0

Mac: 0.13.0 on SAMSON 4.0.0

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Adenita

Publisher: Elisa de Llano

Updated: June 28, 2022


Latest versions

Windows: 0.13.0 on SAMSON 4.0.0

Linux: 0.13.0 on SAMSON 4.0.0

Mac: 0.13.0 on SAMSON 4.0.0

1388
461
Adenita is a toolkit for the modeling and visualization of DNA Nanostructures.

Create, visualize and edit DNA Nanostructures. Work on DNA-protein hybrid structures. Export them to a sequence list, or use the model as input for simulations.

New: join the Adenita community on Discord at https://s-c.io/dntd.

Tutorials

Please check out the Adenita tutorial.

Developers

  • Elisa de Llano
  • Haichao Miao
  • Porting of Adenita to the latest version of SAMSON and its support are done by the SAMSON team at OneAngstrom

References

  • Elisa de Llano, Haichao Miao, Yasaman Ahmadi, Amanda J. Wilson, Morgan Beeby, Ivan Viola, Ivan Barisic. Adenita: Interactive 3D modeling and visualization of DNA Nanostructures. Nucleic Acids Research, Volume 48, Issue 15, September 2020. [Paper]
  • Haichao Miao, Elisa de Llano, Johannes Sorger, Yasaman Ahmadi, Tadija Kekic, Tobias Isenberg, Meister Eduard Gröller, Ivan Barisic, Ivan Viola. Multiscale Visualization and Scale-adaptive Modification of DNA Nanostructures. IEEE Transactions on Visualization and Computer Graphics, 24(1), January 2018. [Paper]
  • Haichao Miao, Elisa de Llano, Tobias Isenberg, Meister Eduard Gröller, Ivan Barisic, Ivan Viola. DimSUM: Dimension and Scale Unifying Maps for Visual Abstraction of DNA Origami Structures. Computer Graphics Forum, 24(1), 37(3), June 2018. [Paper]
  • Rémi Veneziano, Sakul Ratanalert, Kaiming Zhang, Fei Zhang, Hao Yan, Wah Chiu, Mark Bathe. Designer nanoscale DNA assemblies programmed from the top down. Science, 24 Jun 2016. [Paper]
  • Shawn M. Douglas, Adam H. Marblestone, Surat Teerapittayanon, Alejandro Vazquez, George M. Church & William M. Shih. Rapid prototyping of 3D DNA origami shapes with cadnano. Nucleic Acids Research. [Paper]

Known Issues

If you are using an old version of SAMSON and it crashes on Windows after having added Adenita, please make sure you have the latest supported Microsoft Visual C++ Redistributable.

If you encounter any issues, please let us know at SAMSON Connect forum.

What's new

Adenita is now available in the latest version of SAMSON 2021 on all platforms (Windows, Linux, and Mac).

version 0.8.x:

  • Draw DNA strands or DNA nanotubes
  • Load DNA origami structures (created with caDNAno)
  • Create DNA wireframe origami structures (Daedalus algorithm): load a ply file or use the wireframe editor
  • Multi-scale visualization model (from atoms to a corse model)
  • Editing tools: break, connect, twist...
  • Directly work with DNA and protein
  • Explore features of your model with different visualization profiles (melting temperatures, crossovers, GC content...)
  • Export the design as a DNA sequence (.csv)
  • Export to oxDNA configuration and topology files
Adenita is an extension for SAMSON,
the integrated platform for molecular design.

To use Adenita:

1. Create your free account and choose a molecular design plan
2. Download and install SAMSON on your computer
3. Come back to this page to add the extension to your account


When you restart SAMSON, the extension will be automatically installed
and will be usable directly from within SAMSON.