Last year, we published a paper in ACS Omega [1] introducing a restraint-guided inference method that improves ligand stereochemistry on top of Boltz-1. More than half a year has passed since then, and the field has moved quickly: not only has Boltz-2 [2] arrived, but newer models such as Protenix-v1/v2 [3][4] and OpenFold3 [6] have been released in rapid succession. In this post, we re-run our benchmark against these latest models to see how much the ligand-stereochemistry issues we flagged previously have actually improved.

We have launched an English blog for the Computational Drug Discovery and Design Lab.