Protein-ligand Docking tutorials using BioExcel Building Blocks (biobb)
This workflow must be run in biobb.usegalaxy.es. Please, click here to access.
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) 2015-2023 Barcelona Supercomputing Center
- (c) 2015-2023 Institute for Research in Biomedicine
Licensed under the Apache License 2.0, see the file LICENSE for details.
Steps
ID | Name | Description |
---|---|---|
0 | Pdb | biobb_io_pdb_ext |
1 | IdealSdf | biobb_io_ideal_sdf_ext |
2 | ExtractMolecule | biobb_structure_utils_extract_molecule_ext |
3 | BabelConvert | biobb_chemistry_babel_convert_ext |
4 | FpocketRun | biobb_vs_fpocket_run_ext |
5 | StrCheckAddHydrogens | biobb_structure_utils_str_check_add_hydrogens_ext |
6 | BabelConvert | biobb_chemistry_babel_convert_ext |
7 | FpocketFilter | biobb_vs_fpocket_filter_ext |
8 | FpocketSelect | biobb_vs_fpocket_select_ext |
9 | Box | biobb_vs_box_ext |
10 | AutodockVinaRun | biobb_vs_autodock_vina_run_ext |
11 | ExtractModelPdbqt | biobb_vs_extract_model_pdbqt_ext |
12 | BabelConvert | biobb_chemistry_babel_convert_ext |
13 | CatPdb | biobb_structure_utils_cat_pdb_ext |
Outputs
ID | Name | Description | Type |
---|---|---|---|
mypdb.pdb | mypdb.pdb | n/a |
|
myideal_sdf.sdf | myideal_sdf.sdf | n/a |
|
myextract_molecule.pdb | myextract_molecule.pdb | n/a |
|
mybabel_convert.ent | mybabel_convert.ent | n/a |
|
myfpocket_run.zip | myfpocket_run.zip | n/a |
|
myfpocket_run.json | myfpocket_run.json | n/a |
|
mystr_check_add_hydrogens.pdb | mystr_check_add_hydrogens.pdb | n/a |
|
_anonymous_output_1 | _anonymous_output_1 | n/a |
|
myfpocket_filter.zip | myfpocket_filter.zip | n/a |
|
myfpocket_select.pdb | myfpocket_select.pdb | n/a |
|
myfpocket_select.pqr | myfpocket_select.pqr | n/a |
|
mybox.pdb | mybox.pdb | n/a |
|
myautodock_vina_run.log | myautodock_vina_run.log | n/a |
|
myautodock_vina_run.pdbqt | myautodock_vina_run.pdbqt | n/a |
|
myextract_model_pdbqt.pdbqt | myextract_model_pdbqt.pdbqt | n/a |
|
_anonymous_output_2 | _anonymous_output_2 | n/a |
|
mycat_pdb.pdb | mycat_pdb.pdb | n/a |
|
Version History
Version 3 (latest) Created 3rd May 2023 at 14:48 by Genís Bayarri
Update to BioBB 4.0.*
Frozen
Version-3
77034e4
Version 2 Created 22nd Nov 2022 at 10:13 by Genís Bayarri
Frozen
Version-2
3ae56b2
Version 1 (earliest) Created 24th Mar 2022 at 14:58 by Genís Bayarri
Initial commit
Frozen
Version-1
3f50b66
Creators
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Views: 4356 Downloads: 690 Runs: 0
Created: 24th Mar 2022 at 14:58
Last updated: 3rd May 2023 at 14:48
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