Workflow Type: Jupyter

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

This tutorials aim to illustrate the process of protein-ligand docking, step by step, using the BioExcel Building Blocks library (biobb). The particular examples used are based on 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) and Dasatinib (PDB Ligand code 1N1, DrugBank Ligand Code DB01254), small kinase inhibitors molecules used to treat certain types of cancer.

The tutorials will guide you through the process of identifying the active site cavity (pocket) without previous knowledge, and the final prediction of the protein-ligand complex.

Copyright & Licensing

This software has been developed in the MMB group at the BSC & IRB for the European BioExcel, funded by the European Commission (EU H2020 823830, EU H2020 675728).

Licensed under the Apache License 2.0, see the file LICENSE for details.

Version History

Version 5 (latest) Created 4th Mar 2024 at 14:32 by Genís Bayarri

Update to BioBB 4.1.*

Frozen Version-5 23a6546

Version 4 Created 26th Jul 2023 at 10:29 by Genís Bayarri

Fixed importlib_metadata bug

Frozen Version-4 6d4d8a5

Version 3 Created 14th Apr 2023 at 09:15 by Genís Bayarri

Update to BioBB 4.0.*

Frozen Version-3 56cb45e

Version 2 Created 15th Sep 2022 at 12:18 by Genís Bayarri

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

Frozen Version-2 dde48d6

Version 1 (earliest) Created 29th Jun 2021 at 10:19 by Genís Bayarri

Initial commit. Taken from Git commit 1dbc7fe

Frozen Version-1 dcaa743
help Creators and Submitter
Hospital, A., Lowe, D., & Bayarri, G. (2023). Jupyter Notebook Protein-ligand Docking tutorial (PDBe REST API). WorkflowHub.

Views: 3419   Downloads: 639

Created: 29th Jun 2021 at 10:19

Last updated: 14th Apr 2023 at 09:15

help Tags

This item has not yet been tagged.

help Attributions


Total size: 36.4 KB
Powered by
Copyright © 2008 - 2024 The University of Manchester and HITS gGmbH