Tutorial¶

A hands-on notebook that runs a complete virtual screening with the workflows in this repository.

Step	Command	What it does
1	`cavity_analysis`	Extract a protein monomer of interest and perform a cavity analysis with Fpocket
2	`virtual_screening`	Perform a virtual screening on a selected pocket

The tutorial can be run either on Google Colab (no local install) or on a local Jupyter.

Run on Google Colab¶

Click the badge above and run the first setup cell. It builds the biobb_vs_tutorial conda environment from notebooks/colab_environment.yml — nothing to install on your machine. The conda solve is the slow part; run it once and wait.

Run locally¶

Create the environment from notebooks/local_environment.yml, then launch Jupyter from it:

git clone https://github.com/NBDsoftware/biobb_vs_workflows.git
cd biobb_vs_workflows
conda env create -f notebooks/local_environment.yml
conda activate biobb_vs_tutorial
jupyter notebook notebooks/notebook_tutorial.ipynb

The notebook lives at notebooks/notebook_tutorial.ipynb in the repository.