Research Object Crate for Mutation Free Energy Calculations using BioExcel Building Blocks (jupyter notebook)

This tutorial aims to illustrate how to compute a fast-growth mutation free energy calculation, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the Staphylococcal nuclease protein (PDB code 1STN), a small, minimal protein, appropriate for a short tutorial. Workflow engine is a jupyter notebook. Auxiliary libraries used are nb\_conda\_kernels, os, and plotly. Environment setup can be carried out using the environment.yml in the code repository. The tutorial uses docker for running pmx - a local setup can be used instead, see notes in the tutorial.

Author

Genís Bayarri

License

Apache-2.0

Contents