LegoGen

By Scott Michael Louis Slone1, Chris Maffeo1, AbderRahman N Sobh1, Aleksei Aksimentiev1

1. University of Illinois at Urbana-Champaign

Tool workflow for building DNA Brick structures automatically.

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Version 1.1.0b - published on 17 Nov 2016

doi:10.4231/D3M90244C cite this

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Abstract

Legogen is a tool for converting CAD models into DNA nanostructures through the DNA brick method. It provides .pdb and psf files for all-atom molecular dynamics simulations in NAMD, as well as a list of nucleotide sequences for use in experiments. The tool also outputs the coordinates of DNA brick units, called voxels, and a Residue Map file (.resmap) that can be used to build subsequent structures from the same strand library. CAD models can be made inside the Legogen tool with the included 3D graphics software, Blender.

Current Version: 1.1.0

List of Changes

-Public Beta. If you have any questions or find a bug please let us know.

-Can build structures using included templates or manually.

-Included residue Map based on original DNA brick paper

 

 

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Visual Molecular Dynamics (VMD) and Molecular Dynamics (NAMD) developed by the Theoretical and Computational Biophysics Group at the University of Illinois.

Sponsored by

NanoBio Node, University of Illinois Champaign-Urbana

References

Cite this work

Researchers should cite this work as follows:

  • Mechanical Properties of DNA Bricks:
    Scott Michael Slone, Chen-Yu Li, Jejoong Yoo, and Aleksei Aksimentiev. "Molecular mechanics of DNA bricks: in situ structure, mechanical properties and ionic conductivity." New Journal of Physics 18:055012 (2016).

    Original DNA Brick Paper:
    Ke Y, Ong LL, Shih WM, Yin P (2012) Three-dimensional structures self-assembled from DNA bricks. Science
    338(6111):1177–1183.

    Binvox 3D Mesh Voxelizer:
    Min, P. (2004). Binvox 3D Mesh Voxelizer. Retrieved from http://www.cs.princeton.edu/~min/binvox/
    Nooruddin F and Turk G 2003 Simplification and repair of polygonal models using volumetric techniques IEEE Trans. Visual. Comput. Graphics IEEE Transactions on Visualization and Computer Graphics 9 191–205

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

  • Scott Michael Louis Slone; Chris Maffeo; AbderRahman N Sobh; Aleksei Aksimentiev (2016), "LegoGen," https://nanohub.org/resources/legogen. (DOI: 10.4231/D3M90244C).

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