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PoseBusters: Plausibility checks for generated molecule poses.

Paper in Chemical Science and preprint on arXiv

Installation

# install with pip from PyPI
pip install posebusters
<!-- # install with conda from conda-forge conda install posebusters -c conda-forge -->

Usage

<!-- ### Command line 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
<!-- ### Python API ```python from dockbusters import DockBuster # check re-docked ligand DockBuster().bust(ligand_pred_file, ligand_crystal_file, protein_crystal_file) # check docked ligand DockBuster().bust(ligand_pred_file, protein_crystal_file) # check molecule DockBuster().bust(ligand_pred_file, protein_crystal_file) ``` -->

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 paper or preprint:

@article{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.},
  year = "2023",
  publisher = "The Royal Society of Chemistry",
  doi = "10.1039/D3SC04185A",
  url = "http://dx.doi.org/10.1039/D3SC04185A",
}

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: