AutoDock Vina Docking

Dock a ligand library into a receptor (uploaded or fetched by PDB ID) with AutoDock Vina and get ranked binding energies per ligand and per pose.

by Temple Compute

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W-02 · AutoDock Vina Docking

Dock a ligand library into a receptor (uploaded or fetched by PDB ID) with AutoDock Vina and get ranked binding energies per ligand and per pose.

Domain: Drug Discovery

Overview

Docks a ligand library into a receptor (uploaded PDB or fetched from RCSB) with AutoDock Vina. Receptors are prepared with OpenBabel and ligands with Meeko (SMILES are embedded to 3D with RDKit). Output is ranked binding energies per ligand and per pose. The workflow has 3 tasks.

Pipeline

prep    receptor.pdb (or RCSB pdb_id) + ligands ──► results/vina_inputs.tar.gz
dock    AutoDock Vina per ligand                ──► results/docking_out.tar.gz
summary parse affinities                        ──► results/summary.csv + results/poses.csv

Inputs / Outputs

receptor: PDB file, or pdb_id to fetch from RCSB (first-model protein atoms only; hydrogens added at pH 7.4). The example is chain A of 1IEP (Abl kinase).
ligands: one SMILES [name] per line, or a 3D .sdf.
results/summary.csv: one row per ligand, best (most negative) first: rank, ligand, best_affinity_kcal_mol, mean_affinity_kcal_mol, num_poses.
results/poses.csv: one row per pose: ligand, pose, affinity_kcal_mol, rmsd_lb, rmsd_ub.
Ligands that fail to dock are skipped and recorded in manifest.json.

Parameters

| id | Default | Meaning | |---|---|---| | receptor | examples/receptor.pdb | Receptor, used when pdb_id is empty | | pdb_id | empty | 4-character PDB code to fetch instead of the upload | | ligands | examples/ligands.smi | Ligand library (SMILES or SDF) | | box_center | 15.190 53.903 16.917 | Box center X Y Z in Å (1IEP ATP pocket); empty = blind docking on the centroid | | box_size | 20 | Cubic box edge in Å (10-60) | | exhaustiveness | 16 | Vina search effort per ligand (1-64) | | n_poses | 9 | Poses per ligand (1-20) |

box_center must match the receptor used.