Workflow Type: Common Workflow Language
Stable

Protein-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).

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.
  • File
step1_fpocket_select_output_pocket_pdb Output file Path to the PDB file with the cavity found by fpocket.
  • string
step1_fpocket_select_output_pocket_pqr Output file Path to the PQR file with the pocket found by fpocket.
  • string
step1_fpocket_select_config Config file Configuration file for biobb_vs.fpocket_select tool.
  • string
step2_box_output_pdb_path Output file PDB including the annotation of the box center and size as REMARKs.
  • string
step2_box_config Config file Configuration file for biobb_vs.box tool.
  • string
step3_babel_convert_prep_lig_input_path Input file Path to the input file.
  • File
step3_babel_convert_prep_lig_output_path Output file Path to the output file.
  • string
step3_babel_convert_prep_lig_config Config file Configuration file for biobb_chemistry.babel_convert tool.
  • string
step4_str_check_add_hydrogens_input_structure_path Input file Input structure file path.
  • File
step4_str_check_add_hydrogens_output_structure_path Output file Output structure file path.
  • string
step4_str_check_add_hydrogens_config Config file Configuration file for biobb_structure_utils.str_check_add_hydrogens tool.
  • string
step5_autodock_vina_run_output_pdbqt_path Output file Path to the output PDBQT file.
  • string
step5_autodock_vina_run_output_log_path Output file Path to the log file.
  • string
step6_babel_convert_pose_pdb_output_path Output file Path to the output file.
  • string
step6_babel_convert_pose_pdb_config Config file Configuration file for biobb_chemistry.babel_convert tool.
  • string

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.
  • File
step1_fpocket_select_out2 output_pocket_pqr Path to the PQR file with the pocket found by fpocket.
  • File
step2_box_out1 output_pdb_path PDB including the annotation of the box center and size as REMARKs.
  • File
step3_babel_convert_prep_lig_out1 output_path Path to the output file.
  • File
step4_str_check_add_hydrogens_out1 output_structure_path Output structure file path.
  • File
step5_autodock_vina_run_out1 output_pdbqt_path Path to the output PDBQT file.
  • File
step5_autodock_vina_run_out2 output_log_path Path to the log file.
  • File
step6_babel_convert_pose_pdb_out1 output_path Path to the output file.
  • File

Version History

Version 2 (latest) Created 6th Jun 2023 at 15:57 by Genís Bayarri

Updated workflow descriptors


Frozen Version-2 992192c

Version 1 (earliest) Created 10th Jan 2022 at 11:55 by Genís Bayarri

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Frozen Version-1 6fdda20
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Citation
Hospital, A., & Bayarri, G. (2023). CWL Protein-ligand Docking tutorial (Fpocket). WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.259.2
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Views: 1768

Created: 10th Jan 2022 at 11:55

Last updated: 17th Mar 2022 at 10:13

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