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

Workflow Type: Jupyter
Stable

Summary

-- 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

Inputs

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).

Outputs

Output files generated (named according to the input parameters given above):

  • output_structure: generated protein-ligand complex
help Creators and Submitter
Citation
Lowe, D., Bayarri, G., & Hospital, A. (2021). Protein-ligand Docking tutorial using BioExcel Building Blocks (biobb) (jupyter notebook). WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.127.2
Activity

Views: 113   Downloads: 3

Created: 28th Jun 2021 at 11:30

Last updated: 8th Jul 2021 at 10:09

Last used: 30th Jul 2021 at 11:49

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Version History

Version 2 (latest) Created 29th Jun 2021 at 10:06 by Genís Bayarri

Updated to BioBB 3.6.0. Taken from Git commit 1dbc7fe

Version 1 (earliest) Created 28th Jun 2021 at 11:30 by Genís Bayarri

Initial commit. Taken from Git commit 04b4cee

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