Protein-ligand Docking tutorial using BioExcel Building Blocks (biobb)
-- PDB Cluster90 Binding Site Version --
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. Auxiliar libraries used are: nb_conda_kernels, nglview, ipywidgets, plotly, and simpletraj. Environment can be setup using the included environment.yml file.
Parameters needed to configure the workflow:
- pdb_code: PDB code of the experimental complex structure (if exists).
- ligand_code: Ligand PDB code (3-letter code) for the small molecule (e.g. STI).
Output files generated (named according to the input parameters given above):
- output_structure: generated protein-ligand complex
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Created: 28th Jun 2021 at 11:30
Last updated: 8th Jul 2021 at 10:09
Last used: 15th Oct 2021 at 13:45