PoseButcher
"A good butcher always trims the fat"
PoseButcher is a tool for categorising and segmenting virtual hits with reference to experimental protein structures and (fragment) hits.
Ligand atoms are tagged with categories:
- GOOD:
* fragment space: within the fragment bolus
* pocket X: in a specified catalytic/allosteric pocket X
- BAD:
* protein clash: Clashing with the protein
* solvent space: Heading out of the protein/crystal
Usage at a glance
1. Create the butcher (see PoseButcher.__init__):
from posebutcher import PoseButcher
butcher = PoseButcher(protein, hits, pockets)
2. Chop up a posed virtual hit (rdkit.ROMol with a conformer):
result = butcher.chop(mol)
3. Tag a compound based on its pocket occupancy and clashes:
tags = butcher.tag(mol)
4. Explore the expansion opportunities from a given atom in a virtual hit
result = butcher.explore(mol)
5. (Coming soon) Trim a parts of a compound that clash with a protein or leave the crystal
mol = butcher.trim(mol)
6. (Coming soon) Score how well a virtual hit recapitulates shape and colour of the fragment bolus
score: float = butcher.score(mol)
Sample output
Protein, ligand, and catalytic site pockets with Open3D:
A chopped up ligand:
Exploring expansion vector into a desirable pocket
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