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.

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
myideal_sdf.sdf myideal_sdf.sdf n/a
  • File
mypdb.pdb mypdb.pdb n/a
  • File
mybabel_convert.ent mybabel_convert.ent n/a
  • File
myextract_molecule.pdb myextract_molecule.pdb n/a
  • File
_anonymous_output_1 _anonymous_output_1 n/a
  • File
mystr_check_add_hydrogens.pdb mystr_check_add_hydrogens.pdb n/a
  • File
myfpocket_run.json myfpocket_run.json n/a
  • File
myfpocket_run.zip myfpocket_run.zip n/a
  • File
myfpocket_filter.zip myfpocket_filter.zip n/a
  • File
myfpocket_select.pqr myfpocket_select.pqr n/a
  • File
myfpocket_select.pdb myfpocket_select.pdb n/a
  • File
mybox.pdb mybox.pdb n/a
  • File
myautodock_vina_run.log myautodock_vina_run.log n/a
  • File
myautodock_vina_run.pdbqt myautodock_vina_run.pdbqt n/a
  • File
myextract_model_pdbqt.pdbqt myextract_model_pdbqt.pdbqt n/a
  • File
_anonymous_output_2 _anonymous_output_2 n/a
  • File
mycat_pdb.pdb mycat_pdb.pdb n/a
  • File

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

No revision comments

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.296.1
Activity

Views: 888

Created: 24th Mar 2022 at 14:58

Last updated: 3rd May 2023 at 14:48

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