emDNA is a C++ software for minimizing the energy of DNA or DNA+proteins complexes. It can handle various geometrical constraints (e.g. fixed end-to-end distance and/or rotation) and can be used to simulate opened or closed DNA fragments. The project provides a set of command-line tools to perform minimization operations and analyze optimized structures, as well as to assist in sculpting DNA+proteins complexes that can then be optimized.

The modeling and numerical methods are described in the following publications:

• The synergy between protein positioning and DNA elasticity: energy minimization of protein-decorated DNA minicircles (preprint publicly available on arXiv.org)

Contributors

• Nicolas Clauvelin
• Robert Young (Olson lab at Rutgers University)

Pre-build versions

See releases pages.

Build instructions

See build instructions documentation.

Usage instructions

See emDNA usage for details about the commands, options, formatting, and more.

Special Issue: Computational Resources- 2022, Journal of Molecular Biology

In 2021, a manuscript was submitted to the Journal of Molecular Biology for the 2022 Special Issue on Computational Resources. In it included case studies for users. Users can be supplemental instructions, scripts, and optimized data here.

emDNA in Action

See the list below of where emDNA has been used (list updated December 2021):

• Designed architectural proteins that tune DNA looping in bacteria
• Surprising Twists in Nucleosomal DNA with Implication for Higher-order Folding
• Insights into genome architecture deduced from the properties of short Lac repressor-mediated DNA loops