Workflow Type: Unrecognized workflow type
Stable

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. 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

Version History

Version 6 (latest) Created 4th Mar 2024 at 14:30 by Genís Bayarri

Update to BioBB 4.1.*


Frozen Version-6 5cabf1c

Version 5 Created 26th Jul 2023 at 10:27 by Genís Bayarri

Fixed importlib_metadata bug


Frozen Version-5 15c1452

Version 4 Created 14th Apr 2023 at 09:09 by Genís Bayarri

Update to BioBB 4.0.*


Frozen Version-4 b38bf86

Version 3 Created 15th Sep 2022 at 12:15 by Genís Bayarri

Update to BioBB 3.8.*. taken from Git commit 9b31005


Frozen Version-3 d2720e9

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

Updated to BioBB 3.6.0. Taken from Git commit 1dbc7fe


Frozen Version-2 891cdfe

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

Initial commit. Taken from Git commit 04b4cee


Frozen master bc62e24
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.127.1
Activity

Views: 4275   Downloads: 765

Created: 28th Jun 2021 at 11:30

Last updated: 14th Apr 2023 at 09:09

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