Docking

Thanks to advances in biophysics, we are often able to find the structure of proteins from experimental techniques like Cryo-EM or X-ray crystallography. These structures can be powerful aides in designing small molecules. The technique of Molecular docking performs geometric calculations to find a “binding pose” with the small molecule interacting with the protein in question in a suitable binding pocket (that is, a region on the protein which has a groove in which the small molecule can rest). For more information about docking, check out the Autodock Vina paper:

Trott, Oleg, and Arthur J. Olson. “AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading.” Journal of computational chemistry 31.2 (2010): 455-461.

Binding Pocket Discovery

DeepChem has some utilities to help find binding pockets on proteins automatically. For now, these utilities are simple, but we will improve these in future versions of DeepChem.

Pose Generation

Pose generation is the task of finding a “pose”, that is a geometric configuration of a small molecule interacting with a protein. Pose generation is a complex process, so for now DeepChem relies on external software to perform pose generation. This software is invoked and installed under the hood.

Docking

The dc.dock.docking module provides a generic docking implementation that depends on provide pose generation and pose scoring utilities to perform docking. This implementation is generic.

Pose Scoring

This module contains some utilities for computing docking scoring functions directly in Python. For now, support for custom pose scoring is limited.