MDNA is a powerful molecular modeling tool designed to bridge the gap in generating starting structures for DNA and DNA-protein complexes for molecular dynamics (MD) simulations. By leveraging rigid body models, this tool enhances the precision in representing DNA structures, allowing for the inclusion of non-canonical bases, the adjustment of Watson-Crick to Hoogsteen configurations, methylation patterns, and structural extensions. It also provides robust analytical capabilities for MD simulations, calculating geometric properties, curvature, and protein-DNA interaction profiles.
To install MDNA, follow these steps:
git clone --recurse-submodules https://github.com/heezch/mdna.gitAfter that go to the 'mdna' project folder and do:
pip install .See our documentation page
We welcome contributions from the community! To contribute:
- Fork the repository.
- Create a new branch (
git checkout -b feature-branch). - Make your changes and commit them (
git commit -am 'Add new feature'). - Push to the branch (
git push origin feature-branch). - Create a new Pull Request.
Please ensure your code adheres to our coding standards and includes relevant tests.
This project is licensed under the MIT License. See the LICENSE file for details.