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BioExcel Virtual Screening - Protein-Ligand Docking - Cluster90 Binding Site

W-11 · Protein-Ligand Docking (PDB Cluster90 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. 01Create results folder
    Consumes
    src_conda_env_yaml
    Produces
    results_dir
  2. 02Download 3HEC structure from PDB
    Consumes
    results_dir, fetch_pdb_config, src_conda_env_yaml
    Produces
    download_pdb
  3. 03Extract protein structure from downloaded PDB
    Consumes
    download_pdb, src_conda_env_yaml
    Produces
    pdb_protein
  4. 04Download PDB Cluster90 collection for 3HEC
    Consumes
    results_dir, pdb_cluster_zip_config, src_conda_env_yaml
    Produces
    pdb_cluster
  5. 05Extract binding site from Cluster90 collection
    Consumes
    bindingsite_config, pdb_protein, pdb_cluster
    Produces
    output_bindingsite
  6. 06Generate cavity box around binding site
    Consumes
    box_config, output_bindingsite
    Produces
    output_box
  7. 07Download Imatinib (STI) small molecule as SDF
    Consumes
    results_dir, ideal_sdf_config, src_conda_env_yaml
    Produces
    sdf_ideal
  8. 08Convert small molecule from SDF to PDB format
    Consumes
    babel_convert_sdf2pdb_config, sdf_ideal, src_conda_env_yaml
    Produces
    ligand_pdb
  9. 09Prepare ligand for docking (PDB to PDBQT)
    Consumes
    babel_convert_pdb2pdbqt_config, ligand_pdb, src_conda_env_yaml
    Produces
    prep_ligand
  10. 10Prepare receptor protein for docking (PDB to PDBQT)
    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, output_vina_log
  12. 12Extract top docking pose 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_pdbqt2pdb_config, output_pdbqt_model, src_conda_env_yaml
    Produces
    output_pdb_model
  14. 14Combine protein and docked ligand into final 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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