Workflow Type: Galaxy
Stable

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).

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

Inputs

ID Name Description Type
input_pdb_path input_pdb_path runtime parameter for tool FpocketRun n/a
input_pockets_zip input_pockets_zip runtime parameter for tool FpocketFilter n/a
input_summary input_summary runtime parameter for tool FpocketFilter n/a
input_pockets_zip input_pockets_zip runtime parameter for tool FpocketSelect n/a

Steps

ID Name Description
0 IdealSdf biobb_io_ideal_sdf_ext
1 Pdb biobb_io_pdb_ext
2 BabelConvert biobb_chemistry_babel_convert_ext
3 ExtractMolecule biobb_structure_utils_extract_molecule_ext
4 BabelConvert biobb_chemistry_babel_convert_ext
5 StrCheckAddHydrogens biobb_structure_utils_str_check_add_hydrogens_ext
6 FpocketRun biobb_vs_fpocket_run_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
output_sdf_path output_sdf_path n/a
output_pdb_path output_pdb_path n/a
output_path output_path n/a
output_molecule_path output_molecule_path n/a
output_path output_path n/a
output_structure_path output_structure_path n/a
output_pockets_zip output_pockets_zip n/a
output_summary output_summary n/a
output_filter_pockets_zip output_filter_pockets_zip n/a
output_pocket_pdb output_pocket_pdb n/a
output_pocket_pqr output_pocket_pqr n/a
output_pdb_path output_pdb_path n/a
output_pdbqt_path output_pdbqt_path n/a
output_log_path output_log_path n/a
output_pdbqt_path output_pdbqt_path n/a
output_path output_path n/a
output_structure_path output_structure_path n/a

Version History

Version 2 (latest) Created 22nd Nov 2022 at 10:13 by Genís Bayarri

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Frozen Version-2 3ae56b2

Version 1 (earliest) Created 24th Mar 2022 at 14:58 by Genís Bayarri

Initial commit


Frozen Version-1 3f50b66
help Creators and Submitter
Citation
Hospital, A., & Bayarri, G. (2022). Galaxy Protein-ligand Docking tutorial (Fpocket). WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.296.2
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Views: 510

Created: 24th Mar 2022 at 14:58

Last used: 8th Dec 2022 at 16:16

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