Protein-ligand Docking (fpocket) tutorial using BioExcel Building Blocks (biobb) (jupyter notebook)

Version 1

Summary

This tutorial aims to illustrate the process of protein-ligand docking, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the Mitogen-activated protein kinase 14 (p38-α) protein (PDB code 3HEC), a well-known Protein Kinase enzyme, in complex with the FDA-approved Imatinib, (PDB Ligand code STI, DrugBank Ligand Code DB00619), a small molecule kinase inhibitor used to treat certain types of cancer.

Workflow engine is a jupyter notebook. It can be run in binder, following the link given, or locally. Biobb modules used are: biobb_io, biobb_structure_utils, biobb_chemistry, biobb_vs. Auxiliar libraries used are: nb_conda_kernels, nglview, ipywidgets. Environment can be setup using the included environment.yml file.