Monthly Archives: August 2023

A simple criterion can conceal a multitude of chemical and structural sins

We’ve been investigating deep learning-based protein-ligand docking methods which often claim to be able to generate ligand binding modes within 2Å RMSD of the experimental one. We found, however, this simple criterion can conceal a multitude of chemical and structural sins…

DeepDock attempted to generate the ligand binding mode from PDB ID 1t9b
(light blue carbons, left), but gave pretzeled rings instead (white carbons, right).

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Placeholder compounds: distraction vs. accuracy

When showcasing an approach in computational chemistry, an example molecule is required as a placeholder. But which to chose from? I would classify there different approaches: choosing a recognisable molecules, a top selling drugs, or a randomly sketched compound.

At a recent conference, Sheffield Cheminformatics 2023, I saw examples of all three and one problem I had that some placeholders distracted me into searching to figure out what it was.

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