CWL Protein-ligand Docking tutorial (Fpocket)
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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) 2015-2022 Barcelona Supercomputing Center
- (c) 2015-2022 Institute for Research in Biomedicine
Licensed under the Apache License 2.0, see the file LICENSE for details.
Click and drag the diagram to pan, double click or use the controls to zoom.
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| step1_fpocket_select_input_pockets_zip | Input file | Path to the pockets found by fpocket. |
|
| step1_fpocket_select_output_pocket_pdb | Output file | Path to the PDB file with the cavity found by fpocket. |
|
| step1_fpocket_select_output_pocket_pqr | Output file | Path to the PQR file with the pocket found by fpocket. |
|
| step1_fpocket_select_config | Config file | Configuration file for biobb_vs.fpocket_select tool. |
|
| step2_box_output_pdb_path | Output file | PDB including the annotation of the box center and size as REMARKs. |
|
| step2_box_config | Config file | Configuration file for biobb_vs.box tool. |
|
| step3_babel_convert_prep_lig_input_path | Input file | Path to the input file. |
|
| step3_babel_convert_prep_lig_output_path | Output file | Path to the output file. |
|
| step3_babel_convert_prep_lig_config | Config file | Configuration file for biobb_chemistry.babel_convert tool. |
|
| step4_str_check_add_hydrogens_input_structure_path | Input file | Input structure file path. |
|
| step4_str_check_add_hydrogens_output_structure_path | Output file | Output structure file path. |
|
| step4_str_check_add_hydrogens_config | Config file | Configuration file for biobb_structure_utils.str_check_add_hydrogens tool. |
|
| step5_autodock_vina_run_output_pdbqt_path | Output file | Path to the output PDBQT file. |
|
| step5_autodock_vina_run_output_log_path | Output file | Path to the log file. |
|
| step6_babel_convert_pose_pdb_output_path | Output file | Path to the output file. |
|
| step6_babel_convert_pose_pdb_config | Config file | Configuration file for biobb_chemistry.babel_convert tool. |
|
Steps
| ID | Name | Description |
|---|---|---|
| step1_fpocket_select | fpocket_select | Selects a single pocket in the outputs of the fpocket building block.. |
| step2_box | box | This class sets the center and the size of a rectangular parallelepiped box around a set of residues or a pocket. |
| step3_babel_convert_prep_lig | babel_convert | Small molecule format conversion. |
| step4_str_check_add_hydrogens | str_check_add_hydrogens | This class is a wrapper of the Structure Checking tool to add hydrogens to a 3D structure. |
| step5_autodock_vina_run | autodock_vina_run | Wrapper of the AutoDock Vina software. |
| step6_babel_convert_pose_pdb | babel_convert | Small molecule format conversion. |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| step1_fpocket_select_out1 | output_pocket_pdb | Path to the PDB file with the cavity found by fpocket. |
|
| step1_fpocket_select_out2 | output_pocket_pqr | Path to the PQR file with the pocket found by fpocket. |
|
| step2_box_out1 | output_pdb_path | PDB including the annotation of the box center and size as REMARKs. |
|
| step3_babel_convert_prep_lig_out1 | output_path | Path to the output file. |
|
| step4_str_check_add_hydrogens_out1 | output_structure_path | Output structure file path. |
|
| step5_autodock_vina_run_out1 | output_pdbqt_path | Path to the output PDBQT file. |
|
| step5_autodock_vina_run_out2 | output_log_path | Path to the log file. |
|
| step6_babel_convert_pose_pdb_out1 | output_path | Path to the output file. |
|
Version History
Version 2 (latest) Created 6th Jun 2023 at 15:57 by Genís Bayarri
Updated workflow descriptors
Frozen
Version-2992192c
Version 1 (earliest) Created 10th Jan 2022 at 11:55 by Genís Bayarri
Frozen
Version-1
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Creators and Submitter
Views: 2836 Downloads: 633
Created: 10th Jan 2022 at 11:55
Last updated: 17th Mar 2022 at 10:13
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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.
The software stack comes with ...
Teams: BioBB Building Blocks, BioExcel Best Practice Guides
Web page: https://bioexcel.eu/
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 ...
Space: BioExcel
Public web page: https://mmb.irbbarcelona.org/biobb/
