cadnano to PDB File Converter

By Jejoong Yoo1; AbderRahman N Sobh1; Chen-Yu Li1; Aleksei Aksimentiev1

1. University of Illinois at Urbana-Champaign

Accepts CadNano files in the form of *.json and outputs a file in *.pdb which can be read by programs such as VMD.

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Version 1.4c - published on 20 Jul 2016

doi:10.4231/D3SB3X05F cite this

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Abstract

Converts CadNano's paired .json and .csv files into a single .pdb file. Output is formatted as a text file following the standards associated with Protein Data Bank (PDB) files and can be downloaded directly through the Rappture interface.

Credits

The Aksimentiev Group at the University of Illinois

Sponsored by

NanoBio Node, University of Illinois Champaign-Urbana

References

Visualization:

Humphrey, W., Dalke, A. and Schulten, K., "VMD - Visual Molecular Dynamics", J. Molec. Graphics, 1996, vol. 14, pp. 33-38.

Cadnano:

Douglas, Shawn M. (2012). cadnano DNA Origami Software (Version 2) [Computer software]. Cambridge, MA: Massachusetts Institute of Technology. Retrieved January 1, 2014. Available at http://cadnano.org/

Cite this work

Researchers should cite this work as follows:

  • J. Yoo and A. Aksimentiev. In situ structure and dynamics of DNA origami determined through molecular dynamics simulations. Proceedings of the National Academy of Sciences USA 110: 20099-20104 (2013).

  • Jejoong Yoo, AbderRahman N Sobh, Chen-Yu Li, Aleksei Aksimentiev (2016), "cadnano to PDB File Converter," https://nanohub.org/resources/cadnanocvrt. (DOI: 10.4231/D3SB3X05F).

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Tags

  1. CadNano
  2. Modeling nanomaterials
  3. nano/bio
  4. NanoBio Node at Illinois
  5. proteins
  6. Scalable Molecular Dynamics (NAMD)
  7. simulation and modeling
  8. Visual Molecular Dynamics (VMD)