PoseButcher 0.0.6

A tool for categorising and segmenting virtual hits with reference to experimental protein structures and (fragment) hits.

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. (Coming soon) Trim a parts of a compound that clash with a protein or leave the crystal

	mol = butcher.trim(mol)

5. (Coming soon) Explore the expansion opportunities from a given atom in a virtual hit

	result = butcher.explore(mol, index, direction)

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, fragment bolus, and catalytic pockets with Open3D:

A chopped up ligand:

Installation

1. Install PoseButcher:

pip install posebutcher

Examples

PoseButcher ships with some open access test data from the XChem group at Diamond Light Source, funded by the ASAP consortium.

To run the "example.ipynb":

git clone [e-mail]:mwinokan/PoseButcher
cd PoseButcher
jupyter lab