Protein-Ligand Docking into an fpocket Cavity

Dock a ligand with AutoDock Vina into a cavity found by fpocket.

by Temple Compute

Run Protein-Ligand Docking into an fpocket Cavity on Horus

W-13 · Protein-Ligand Docking into an fpocket Cavity

Dock a ligand with AutoDock Vina into a cavity found by fpocket.

Domain: BioExcel Building Blocks

Overview

Docks one ligand into a receptor with AutoDock Vina (default p38-alpha MAP kinase, PDB 3HEC, imatinib STI). fpocket detects cavities on the receptor, which are filtered by druggability and volume; the chosen pocket defines the docking box. The top pose is assembled into a complex. The workflow has 14 tasks.

Pipeline

fetch_pdb                    Download pdb_id or use the uploaded receptor
extract_protein              Remove ligands, ions, water
fpocket_run                  Detect cavities
fpocket_filter               Filter by druggability and volume
fpocket_select               Extract the chosen pocket
box                          Docking box around the cavity
str_check_add_hydrogens      Receptor PDBQT
ideal_sdf                    Download ligand_code as SDF, or use the upload
babel_convert_sdf_to_pdb     SDF to PDB
babel_convert_pdb_to_pdbqt   Ligand PDBQT
autodock_vina_run            Docking
extract_model_pdbqt          Top pose
babel_convert_pdbqt_to_pdb   Pose to PDB
cat_pdb                      Receptor + pose complex

Inputs / Outputs

Inputs: pdb_id or, when empty, the structure upload; the ligand by code or SDF.
Outputs (results/): download.pdb, pdb_protein.pdb, fpocket_all_pockets.zip, fpocket_summary.json, fpocket_filter_pockets.zip, fpocket_cavity.pdb, fpocket_pocket.pqr, box.pdb, ideal.sdf, ligand.pdb, prep_ligand.pdbqt, prep_receptor.pdbqt, output_vina.pdbqt, output_model.pdbqt, output_model.pdb, output_structure.pdb.

Parameters

| id | Default | Meaning | |---|---|---| | pdb_id | 3HEC | RCSB PDB code; clear it to use structure | | structure | examples/3hec.pdb | Receptor used when pdb_id is empty | | min_druggability | 0 | Cavities with a lower fpocket druggability score are dropped (0-1); at 0 no druggability filter is applied | | min_volume | 800 | Smaller cavities (Å³) are dropped (0-5000) | | max_volume | 2000 | Larger cavities (Å³) are dropped; keep it above min_volume (100-20000) | | pocket | 6 | fpocket rank (after the cavity filter) of the pocket that defines the box; differs per receptor | | box_offset_a | 12 | Padding around the pocket on each side of the box (A) | | ligand_code | STI | Ligand to dock, as PDB code; clear it to use ligand_sdf | | ligand_sdf | examples/sti_ideal.sdf | 3D SDF used when ligand_code is empty |