cadnano to PDB File Converter

By Jejoong Yoo; 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.

Launch Tool

This tool version is unpublished and cannot be run. If you would like to have this version staged, you can put a request through HUB Support.

Archive Version 1.1
Published on 12 Aug 2014 All versions

doi:10.4231/D3319S36K cite this

This tool is closed source.

Category

Tools

Published on

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/D3319S36K).

    BibTex | EndNote

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)