This repository provides a streamlined pipeline to compute binding affinities for protein–ligand complexes generated by AlphaFold3. It takes the AlphaFold3-style JSON input containing protein sequence and ligand SMILES, reconstructs the 3D structure, prepares it for docking, and runs AutoDock Vina to calculate the binding affinity.
- Accepts AlphaFold3-style JSON input files (e.g.,
fold_input.json) - Automatically extracts protein and ligand information
- Converts ligand SMILES to 3D with Open Babel
- Adds polar hydrogens to protein and ligand
- Automatically generates grid box around binding site
- Performs docking using AutoDock Vina
- Outputs predicted binding energy (kcal/mol)
Before using the pipeline, make sure the following dependencies are installed:
- Python ≥ 3.7
wget(Linux/Mac)autodock-vina(Vina 1.2.x or newer)openbabel(for SMILES to PDBQT conversion)
Install with:
apt-get update
apt-get install -y openbabel autodock-vina wget
pip install "numpy<3.0"
pip install biopython rdkit-pypi mdanalysis MDAnalysisTests
python docking.py gsh.cif --ligand_resname LIG --num_modes 5