Skip to main content

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

Project description

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:

butcher_3d

A chopped up ligand:

butcher_2d

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 git@github.com:mwinokan/PoseButcher
cd PoseButcher
jupyter lab

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

posebutcher-0.0.9.tar.gz (13.3 kB view hashes)

Uploaded Source

Built Distribution

posebutcher-0.0.9-py3-none-any.whl (14.6 kB view hashes)

Uploaded Python 3

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page