Virtual Screening - Protein-Ligand Docking via EBI PDBe API (p38-alpha / Dasatinib)

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 3LFA structure from PDB (protein + ligand complex)

   Consumes

   download_pdb_config, src_conda_env_yaml

   Produces

   downloaded_pdb

2. 02Extract protein chain (remove ligands, water, ions)

   Consumes

   downloaded_pdb, src_conda_env_yaml

   Produces

   pdb_protein

3. 03Query PDBe REST-API for binding sites (residues.json)

   Consumes

   get_binding_sites_config

   Produces

   residues_json

4. 04Generate docking box around selected binding site cavity

   Consumes

   generate_cavity_box_config, downloaded_pdb

   Produces

   output_box

5. 05Download Dasatinib (1N1) ideal SDF from PDBe

   Consumes

   download_ligand_sdf_config, src_conda_env_yaml

   Produces

   sdf_ideal

6. 06Convert ligand SDF to PDB format (OpenBabel)

   Consumes

   convert_sdf_to_pdb_config, sdf_ideal, src_conda_env_yaml

   Produces

   ligand_pdb

7. 07Convert ligand PDB to PDBQT for AutoDock Vina (OpenBabel)

   Consumes

   prepare_ligand_pdbqt_config, ligand_pdb, src_conda_env_yaml

   Produces

   prep_ligand

8. 08Add hydrogens and convert receptor to PDBQT for AutoDock Vina

   Consumes

   prepare_receptor_pdbqt_config, pdb_protein, src_conda_env_yaml

   Produces

   prep_receptor

9. 09Run AutoDock Vina protein-ligand docking

   Consumes

   prep_ligand, prep_receptor, output_box

   Produces

   output_vina_pdbqt, output_vina_log

10. 10Extract best docking pose (model 1) from Vina output

    Consumes

    extract_docking_pose_config, output_vina_pdbqt

    Produces

    output_pdbqt_model

11. 11Convert docking pose PDBQT to PDB format (OpenBabel)

    Consumes

    convert_pose_to_pdb_config, output_pdbqt_model, src_conda_env_yaml

    Produces

    output_pdb_model

12. 12Merge receptor and docking pose into final protein-ligand complex PDB

    Consumes

    downloaded_pdb, output_pdb_model, src_conda_env_yaml

    Produces

    output_structure