PoseBusters: Plausibility checks for generated molecule poses.
PoseBusters is a command line tool and Python library to check the output of molecular conformation generators, docking programs, or other programs that generate molecules in 3D.
Quick start
PoseBusters can be installed from PyPI.
>>> pip install posebusters
Use the bust
command to check molecules, docked ligands or generated molecules conditioned on a protein.
>>> bust redocked_ligand.sdf -l crystal_ligand.sdf -p protein.pdb --outfmt short
redocked_ligand.sdf redocked_ligand passes (25 / 25)
...
>>> bust redocked_ligand.sdf -l crystal_ligand.sdf -p protein.pdb --outfmt long
Long summary for redocked_ligand.sdf redocked_ligand
MOL_PRED loaded .
MOL_TRUE loaded .
MOL_COND loaded .
Sanitization .
All atoms connected .
Molecular formula .
Molecular bonds .
Double bond stereochemistry .
Tetrahedral chirality .
Bond lengths .
Bond angles .
...
>>> bust redocked_ligand.sdf -l crystal_ligand.sdf -p protein.pdb --outfmt csv
file,molecule,mol_pred_loaded,mol_true_loaded,mol_cond_loaded,sanitization,all_atoms_connected,molecular_formula,molecular_bonds,double_bond_stereochemistry,tetrahedral_chirality,bond_lengths,bond_angles,internal_steric_clash,aromatic_ring_flatness,double_bond_flatness,internal_energy,protein-ligand_maximum_distance,minimum_distance_to_protein,minimum_distance_to_organic_cofactors,minimum_distance_to_inorganic_cofactors,minimum_distance_to_waters,volume_overlap_with_protein,volume_overlap_with_organic_cofactors,volume_overlap_with_inorganic_cofactors,volume_overlap_with_waters,rmsd_≤_2å
redocked_ligand.sdf,redocked_ligand,True,True,True,True,True,True,True,True,True,True,True,True,True,True,True,True,True,True,True,True,True,True,True,True,True
...
For more usage examples, bulk processing, and the Python API see the documentation for the command line tool and the Python library.
Docking methods comparison
For more detailed 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}
}
Sample checks
For more information on the checks, see Checks.
Steric clash |
|
Bad: Molecule intertwined and atoms clashing |
Good: |
Aromatic rings flatness |
|
Bad: Conjugated pi bond systems should be flat |
Good: |
Volume overlap |
|
Bad: Ligand and receptor clash |
Good: |
For more information on the checks, see Checks.