Interactive Jupyter Notebooks for FAIR and reproducible biomolecular simulation workflows

Interactive Jupyter Notebooks in combination with Conda environments can be used to generate FAIR (Findable, Accessible, Interoperable and Reusable/Reproducible) biomolecular simulation workflows. The interactive programming code accompanied by documentation, and the possibility to inspect intermediate results with versatile graphical charts and data visualization is very helpful, especially in iterative processes, where parameters might be adjusted to a particular system of interest. This work presents a collection of FAIR notebooks covering different areas of the biomolecular simulation field, such as Molecular Dynamics (MD), protein-ligand docking, molecular checking/modeling, molecular interactions and free energy perturbations. Workflows can be launched with myBinder or easily installed in a local system. The collection of notebooks aims to be a compilation of demonstration workflows, and is continuously updated and expanded with examples using new methodologies and tools.

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Created: 5th Mar 2024 at 09:29

Last updated: 5th Mar 2024 at 09:34

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