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Adenita

Publisher: Elisa de Llano

Updated: December 11, 2019


Latest versions

Windows: 0.8.1 on SAMSON 0.8.5

Linux: 0.8.1 on SAMSON 0.8.5

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Adenita

Publisher: Elisa de Llano

Updated: December 11, 2019


Latest versions:

- Windows: 0.8.1 on SAMSON 0.8.5

- Linux: 0.8.1 on SAMSON 0.8.5

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.

Developers

  • Elisa de Llano
  • Haichao Miao

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. Pre-print at bioRxiv, November 2019. [Pre-print]
  • 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 SAMSON crashes after having added Adenita, please make sure you have the latest supported Microsoft Visual C++ Redistributable. If the problem persists, or you encounter other bugs, please let us know at Samson's forum or the corresponding github repository (Windows or Linux).

What's new

  • 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