Protein-Ligand Docking with a Cluster90 Binding Site

Dock a ligand with AutoDock Vina into a binding site inferred from PDB Cluster90 homologs.

by Temple Compute

Run Protein-Ligand Docking with a Cluster90 Binding Site on Horus

W-11 · Protein-Ligand Docking with a Cluster90 Binding Site

Dock a ligand with AutoDock Vina into a binding site inferred from PDB Cluster90 homologs.

Domain: BioExcel Building Blocks

Overview

Docks one ligand into a receptor with AutoDock Vina (default p38-alpha MAP kinase, PDB 3HEC, imatinib STI). The docking box is placed where the site_ligand binds across the Cluster90 homologs of the receptor. The top pose is assembled into a protein-ligand complex. The workflow has 14 tasks.

Pipeline

create_results_folder     Create results folder
fetch_pdb                 Download pdb_id
extract_molecule          Extract protein
pdb_cluster_zip           Download the Cluster90 collection
bindingsite               Extract binding site from the collection
box                       Docking box around the site
ideal_sdf                 Download ligand_code as SDF, or use the upload
babel_convert_sdf2pdb     SDF to PDB
babel_convert_pdb2pdbqt   Ligand PDBQT
str_check_add_hydrogens   Receptor PDBQT
autodock_vina_run         Docking
extract_model_pdbqt       Top pose
babel_convert_pdbqt2pdb   Pose to PDB
cat_pdb                   Protein + ligand complex

Inputs / Outputs

Inputs: pdb_id (receptor, no upload) and the ligand by code or SDF.
Outputs (results/): download.pdb, pdb_protein.pdb, pdb_cluster.zip, bindingsite.pdb, 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 | 3HEC | Receptor PDB code; its Cluster90 homologs define the site | | site_ligand | STI | Ligand whose pose in the homologs defines the site; must bind a homolog | | 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 | | box_offset_a | 12 | Padding around the site on each side of the box (A) |