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Software module for DNA structure generation and analysis

This site contains the project documentation for the mdna project that is python toolkit for the structure generation and analysis of DNA molecular dynamics simulations.

Table Of Contents

  1. Quick Start
  2. Tutorials
  3. Explanation
  4. Jupyter Notebooks
  5. Modules
  6. API reference

Quickly find what you're looking for depending on your use case by looking at the different pages.

Three examples that highlight the building of biomolecular assemblies with mdna. Here we showcase the extension of DNA structures, using proteins as scaffold to generate DNA structure, and lastly to connect two DNA strands to form a DNA loop. Molecular representations are visualized with Mol* Viewer.

Image 1 Image 2 Image 3

Citation

Link to the publication

What is MDNA?

mdna is a Python toolkit for atomic resolution generation and analysis of double stranded DNA structures. It enables the construction of arbitrarily shaped DNA using spline based mapping, supports canonical and non canonical nucleotides, and integrates Monte Carlo relaxation to obtain physically consistent configurations.

In addition to structure generation, MDNA implements rigid base parameter analysis and linking number calculations, and exports directly to MDTraj compatible trajectories for molecular dynamics workflows.

Key Features

•   Arbitrary DNA shape generation via spline control points
•   Sequence driven construction with canonical and non canonical bases
•   Hoogsteen base flipping and methylation editing
•   Circular DNA generation with linking number control
•   Monte Carlo based structure relaxation
•   Native rigid base parameter analysis
•   Intra base pair: shear, stretch, stagger, buckle, propeller, opening
•   Inter base pair step: shift, slide, rise, tilt, roll, twist

Acknowledgements

This project is supported by the NWO Klein grant.