Protein-Ligand Docking with PDBe Binding Sites

Dock a ligand with AutoDock Vina into the binding site PDBe annotates for a chosen ligand.

by Temple Compute

Run Protein-Ligand Docking with PDBe Binding Sites on Horus

W-12 · Protein-Ligand Docking with PDBe Binding Sites

Dock a ligand with AutoDock Vina into the binding site PDBe annotates for a chosen ligand.

Domain: BioExcel Building Blocks

Overview

Docks one ligand into a receptor with AutoDock Vina (default p38-alpha MAP kinase, PDB 3LFA, dasatinib 1N1). The docking box comes from the PDBe REST API binding-site annotation of site_ligand; the top pose is assembled into a protein-ligand complex. The workflow has 13 tasks.

Pipeline

download_pdb              Download pdb_id
extract_protein           Remove ligands, water, ions
get_binding_sites         Query PDBe REST API (residues.json)
select_binding_site       Pick the site of site_ligand (scripts/select_site.py)
generate_cavity_box       Docking box around the site residues
download_ligand_sdf       Download ligand_code as SDF, or use the upload
convert_sdf_to_pdb        SDF to PDB
prepare_ligand_pdbqt      Ligand PDBQT
prepare_receptor_pdbqt    Receptor PDBQT
run_docking               AutoDock Vina
extract_docking_pose      Top pose
convert_pose_to_pdb       Pose to PDB
assemble_complex          Receptor + pose complex

Inputs / Outputs

Inputs: pdb_id (receptor, no upload) and the ligand by code or SDF.
Outputs (results/): download.pdb, pdb_protein.pdb, residues.json, box.pdb, ideal.sdf, ligand.pdb, prep_ligand.pdbqt, prep_receptor.pdbqt, output_vina.pdbqt, output_vina.log, output_model.pdbqt, output_model.pdb, output_structure.pdb.

Parameters

| id | Default | Meaning | |---|---|---| | pdb_id | 3LFA | Receptor PDB code; its PDBe binding sites are used | | site_ligand | 1N1 | Ligand whose PDBe site defines the box; the run stops and lists the available sites if there is none | | ligand_code | 1N1 | Ligand to dock, as PDB code; clear it to use ligand_sdf | | ligand_sdf | examples/1n1_ideal.sdf | 3D SDF used when ligand_code is empty | | box_offset_a | 12 | Padding around the site residues on each side of the box (A) |