PoseBusters: Plausibility checks for generated molecule poses.
Project description
PoseBusters: Plausibility checks for generated molecule poses.
Paper in Chemical Science and preprint 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 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:
- RDKit - https://github.com/rdkit/rdkit
- Pandas - https://github.com/pandas-dev/pandas
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