Using interactive Jupyter Notebooks and BioConda for FAIR and reproducible biomolecular simulation workflows.

ABSTRACT: 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 various 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

SUBMITTER: Bayarri G 

PROVIDER: S-EPMC11189206 | biostudies-literature | 2024 Jun

REPOSITORIES: biostudies-literature