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BioExcel Virtual Screening - Protein-Ligand Docking with fpocket (p38α / Imatinib)

W-13 · Protein-Ligand Docking (Fpocket Binding Site)

v114 stages0 clones0

The pipeline

Every stage picks its own compute target. Temple Compute OS resolves the dependencies between them and moves the data across each boundary.

  1. 01Download 3HEC structure from PDB
    Consumes
    fetch_pdb_config, src_conda_env_yaml
    Produces
    download_pdb
  2. 02Extract protein structure (remove ligands, ions, water)
    Consumes
    download_pdb, src_conda_env_yaml
    Produces
    pdb_protein
  3. 03Compute protein cavities with fpocket
    Consumes
    fpocket_run_config, pdb_protein
    Produces
    fpocket_all_pockets, fpocket_summary
  4. 04Filter protein cavities by volume (800-2000 ų)
    Consumes
    fpocket_filter_config, fpocket_all_pockets, fpocket_summary
    Produces
    fpocket_filter_pockets
  5. 05Extract selected pocket cavity (pocket 6)
    Consumes
    fpocket_select_config, fpocket_filter_pockets
    Produces
    fpocket_cavity, fpocket_pocket
  6. 06Generate docking box around selected cavity (offset 12 Å)
    Consumes
    box_config, fpocket_pocket
    Produces
    output_box
  7. 07Download Imatinib (STI) small molecule in SDF format
    Consumes
    ideal_sdf_config, src_conda_env_yaml
    Produces
    sdf_ideal
  8. 08Convert small molecule from SDF to PDB format
    Consumes
    babel_convert_sdf_to_pdb_config, sdf_ideal, src_conda_env_yaml
    Produces
    ligand_pdb
  9. 09Prepare ligand for docking (PDB to PDBQT, add partial charges)
    Consumes
    babel_convert_pdb_to_pdbqt_config, ligand_pdb, src_conda_env_yaml
    Produces
    prep_ligand
  10. 10Prepare receptor protein for docking (PDB to PDBQT, add charges)
    Consumes
    str_check_add_hydrogens_config, pdb_protein, src_conda_env_yaml
    Produces
    prep_receptor
  11. 11Run AutoDock Vina docking
    Consumes
    prep_ligand, prep_receptor, output_box
    Produces
    output_vina_pdbqt
  12. 12Extract docking pose (model 1) from Vina output
    Consumes
    extract_model_pdbqt_config, output_vina_pdbqt
    Produces
    output_pdbqt_model
  13. 13Convert docking pose from PDBQT to PDB format
    Consumes
    babel_convert_pdbqt_to_pdb_config, output_pdbqt_model, src_conda_env_yaml
    Produces
    output_pdb_model
  14. 14Superpose ligand docking pose onto target protein structure
    Consumes
    pdb_protein, output_pdb_model, src_conda_env_yaml
    Produces
    output_structure

Run this workflow

This release is frozen and self-contained: the pipeline definition, its input files, and its plugin environment. Open it in Temple Compute OS to clone it into your own account and run it on HPC or any cloud. Temple Compute OS is in private beta, so you will need an invitation first.

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