A repository for visualizing the free energy landscape after randomly docking ligands to proteins.
The following Python packages are required to run these scripts:
- pymol
- biopython
- rdkit
- openbabel
- scikit-learn
- numpy
Installation: pip install -r requirements.txt
Converts protein CIF files to PDBQT files. Usage:
python cif_to_pdbqt.py "CIF file path"
Converts protein PDB files to PDBQT files. Usage:
python pdb_to_pdbqt.py "PDB file path"
Converts SMILES format ligands to PDBQT files. Usage:
python smiles_to_pdbqt.py "SMILES"
Performs random docking using ligand and protein PDB and PDBQT files. Usage:
python random_docking.py "protein_pdbqt" "ligand_pdbqt" "protein_pdb"
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"
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.