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Protein Preparation in Jupyter - 2024 Mini-Workshop
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Today, Jupyter notebooks are everything you need to prepare a molecular dynamics simulation. Not only do they provide a unified interface to all the tools needed to prepare and visualize a simulation, they also provide an easy way to record, repeat, and even publish your workflow, including any alterations needed for a particularly stubborn system.
This workshop covers the preparation of a protein system from a structure downloaded from the PDB, entirely in the Jupyter notebook, complete with 3D visualizations at every step of the way. We hope to make it accessible even to new MD practitioners, assuming they have some familiarity with Python.
This workshop covers the preparation of a protein system from a structure downloaded from the PDB, entirely in the Jupyter notebook, complete with 3D visualizations at every step of the way. We hope to make it accessible even to new MD practitioners, assuming they have some familiarity with Python.
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