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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Jupyter Notebook Protein MD Setup tutorial
- Added 9 months ago -
Jupyter Notebook GMX Notebook Automatic Ligand Parameterization tutorial
- Added 9 months ago -
Jupyter Notebook Protein Ligand Complex MD Setup tutorial
- Added 9 months ago -
Jupyter Notebook Mutation Free Energy Calculations
- Added 9 months ago -
Jupyter Notebook Protein-ligand Docking tutorial (Cluster90)
- Added 9 months ago -
Jupyter Notebook Protein-ligand Docking tutorial (PDBe REST API)
- Added 9 months ago -
Jupyter Notebook Protein-ligand Docking tutorial (Fpocket)
- Added 9 months ago -
Jupyter Notebook Classical Molecular Interaction Potentials
- Added 9 months ago -
Jupyter Notebook Protein conformational ensembles generation
- Added 9 months ago -
Jupyter Notebook Macromolecular Coarse-Grained Flexibility tutorial
- Added 9 months ago -
Jupyter Notebook Protein Conformational Transitions calculations tutorial
- Added 9 months ago -
Jupyter Notebook Amber Protein MD Setup tutorial
- Added 9 months ago -
Jupyter Notebook Amber Protein Ligand Complex MD Setup tutorial
- Added 9 months ago -
Jupyter Notebook Amber Constant pH MD Setup tutorial
- Added 9 months ago -
Jupyter Notebook ABC MD Setup tutorial
- Added 9 months ago -
Jupyter Notebook Structural DNA helical parameters tutorial
- Added 9 months ago -
Jupyter Notebook Molecular Structure Checking
- Added 9 months ago
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Created: 5th Mar 2024 at 09:29
Last updated: 5th Mar 2024 at 09:34