The notebook generate_analogs_and_dock.ipynb has an example which performs the following tasks
- Generate analogs with REINVENT4
- Filter the ligands generated by REINVENT4
- Generate conformers for the ligands
- Prepare a protein for docking
- Dock the ligands
- Generate interaction fingerprints for the docked ligands
The notebook requires the following
- REINVENT4
- Spruce, Omega2, and Hybrid from OpenEye scientific software
pip install rdkit mols2grid useful_rdkit_utils prolif seaborn
The file data/fragment_lead_pairs.csv was taken from https://pubs.acs.org/doi/10.1021/acs.jmedchem.3c02070