Biomodeling: Holliday Junction
Intro
Free energy landscape in Ramachandran space.
Metadynamics, REMD, etc.
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References
Yoo, J. & Aksimentiev, A. Molecular Dynamics of Membrane-Spanning DNA Channels: Conductance Mechanism, Electro-Osmotic Transport, and Mechanical Gating. Journal of Physical Chemistry Letters 6, 4680-4687 (2015). https://doi.org/10.1021/acs.jpclett.5b01964
Yoo, J. & Aksimentiev, A. In situ structure and dynamics of DNA origami determined through molecular dynamics simulations. Proceedings of the National Academy of Sciences of the United States of America 110, 20099-20104 (2013). https://doi.org/10.1073/pnas.1316521110
Installation of Cadnano2
conda create -n cadnano2
conda activate cadnano2
conda install -c anaconda pip
pip install cadnano2
cadnano2