Molecule depiction in Squonk

Tim Dudgeon 2024-02-01

Squonk

In my last post I talked about how you can use Squonk jobs to calculate properties of molecule. Another useful thing it can do is molecule depiction, including the ability to display atomic properties. The basic flow is to run a job that does the calculations and then run the Depict molecules job to generate graphics of those molecules.

There are number of depiction features.

Basic molecule depiction:

Atom highlighting:

Maximum common substructure (MCS) highlighting:

MCS and atom highlighting:

Atom properties:

Multiple molecules can be displayed as a grid. As an example here are atomic pKa values highlighed and displayed: The pKa values were calculated using ChemAxon’s pKa calculator (note you need a ChemAxon license for that).

A complete example (in this case illustrating how to display sites of Cytochrome P450 metabolism predicted using the SmartCYP job) can be found here.

Here is documentation on using the Depict molecules job

Access Squonk here. You can register for an account.

The actual depiction is done using CDK’s Depiction generator which is a great tool for generating high quality molecular images.