Random Energy Dock

A repository for visualizing the free energy landscape after randomly docking ligands to proteins.

Requirements

The following Python packages are required to run these scripts:

• pymol
• biopython
• rdkit
• openbabel
• scikit-learn
• numpy

Installation: pip install -r requirements.txt

Script Descriptions

cif_to_pdbqt.py

Converts protein CIF files to PDBQT files. Usage:

python cif_to_pdbqt.py "CIF file path"

pdb_to_pdbqt.py

Converts protein PDB files to PDBQT files. Usage:

python pdb_to_pdbqt.py "PDB file path"

smiles_to_pdbqt.py

Converts SMILES format ligands to PDBQT files. Usage:

python smiles_to_pdbqt.py "SMILES"

random_docking.py

Performs random docking using ligand and protein PDB and PDBQT files. Usage:

python random_docking.py "protein_pdbqt" "ligand_pdbqt" "protein_pdb"

visualize_energy_pymol.py

Calculates binding free energy from docking results and visualizes it using PyMOL. Usage:

python visualize_energy_pymol.py "protein PDB file path" "PDBQT_file_path/docking_output_*.pdbqt"

Visualization

The following image is an example of a protein-ligand docking visualization created by this tool. The red dots represent regions where the binding free energy is stable, indicating potential binding sites.