PoseButcher 0.0.9

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 --upgrade posebutcher

N.B. open3d version 0.18 or greater is required

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