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