Jupyter Notebook Protein-ligand Docking tutorial (PDBe REST API)
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Download RO-CrateProtein-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).
- (c) 2015-2025 Barcelona Supercomputing Center
- (c) 2015-2025 Institute for Research in Biomedicine
Licensed under the Apache License 2.0, see the file LICENSE for details.
Version History
Version 6 (latest) Created 6th Aug 2025 at 10:49 by Genís Bayarri
Update to BioBB 5.1.*
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Version-6757fce2
Version 5 Created 4th Mar 2024 at 14:32 by Genís Bayarri
Update to BioBB 4.1.*
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Version-5
23a6546
Version 4 Created 26th Jul 2023 at 10:29 by Genís Bayarri
Fixed importlib_metadata bug
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Version-4
6d4d8a5
Version 3 Created 14th Apr 2023 at 09:15 by Genís Bayarri
Update to BioBB 4.0.*
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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
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Version-2
dde48d6
Version 1 (earliest) Created 29th Jun 2021 at 10:19 by Genís Bayarri
Initial commit. Taken from Git commit 1dbc7fe
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Version-1
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Creators and Submitter
Views: 8390 Downloads: 2831
Created: 29th Jun 2021 at 10:19
Last updated: 6th Aug 2025 at 10:51
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https://orcid.org/0000-0003-0513-0288
BioExcel is the leading European Centre of Excellence for Computational Biomolecular Research. Established in 2015, the centre has grown into a major research and innovation hub for scientific computing. BioExcel develops some of the most popular applications for modelling and simulations of biomolecular systems. A broad range of additional pre-/post-processing tools are integrated with the core applications within user-friendly workflows and container solutions.
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The BioExcel Building Blocks (biobb) software library is a collection of Python wrappers on top of popular biomolecular simulation tools. This library offers a layer of interoperability between the wrapped tools, which make them compatible and prepared to be directly interconnected to build complex biomolecular workflows. The building blocks can be used in many different workflow systems, including Galaxy, CWL, Jupyter Notebook and PyCOMPSs – notably their ...
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Public web page: https://mmb.irbbarcelona.org/biobb/
Interactive Jupyter Notebooks in combination with Conda environments can be used to generate FAIR (Findable, Accessible, Interoperable and Reusable/Reproducible) biomolecular simulation workflows. The interactive programming code accompanied by documentation, and the possibility to inspect intermediate results with versatile graphical charts and data visualization is very helpful, especially in iterative processes, where parameters might be adjusted to a particular system of interest. This work ...
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