PoseBusters: Plausibility checks for generated molecule poses.

Paper on arXiv

Installation

# install with pip from PyPI
pip install posebusters

Usage

# Check generated molecule pose.
bust molecule_pred.sdf
bust molecule_a.sdf molecule_b.sdf
bust molecule_*.sdf

# Check new ligand generated for a given protein.
bust ligand_pred.sdf -p mol_cond.pdb

# Check re-docked ligand (a pose that should recover the ligand in a given protein-ligand crystal complex).
bust ligand_pred.sdf -l mol_true.sdf -p protein.pdb

# Check any of the three by providing a csv with files to check together
bust -t file_table.csv

Documentation

Documentation is available at https://posebusters.readthedocs.io.

For more information about the tests and for a study using PoseBusters to compare docking methods, refer to our preprint:

@online{buttenschoen2023posebusters,
  title = {{{PoseBusters}}: {{AI-based}} Docking Methods Fail to Generate Physically Valid Poses or Generalise to Novel Sequences},
  shorttitle = {{{PoseBusters}}},
  author = {Buttenschoen, Martin and Morris, Garrett M. and Deane, Charlotte M.},
  date = {2023-08-10},
  eprint = {2308.05777},
  eprinttype = {arxiv}
}

The data used for the paper is available at https://zenodo.org/record/8278563.

Feedback & Contact

We welcome all feedback. For code issues, please open an issue. For other inquiries contact us by email.

Thanks

This program uses software written by other people. Notably:

• RDKit - https://github.com/rdkit/rdkit
• Pandas - https://github.com/pandas-dev/pandas