DeepMind's SynthID Bio watermarks ai-designed proteins that still work in the lab

On 30 September Google DeepMind published SynthID Bio, a way of hiding an invisible, detectable watermark in ai-designed proteins. It nudges the choice of amino acids in a sequence, and adjusts atomic coordinates in predicted 3D structures, using a version built into part of AlphaFold 3.

In wet-lab tests against three targets (VEGF-A, the SARS-CoV-2 spike protein and PD-L1), watermarked protein binders matched unwatermarked ones on hit rate, binding strength and sequence diversity. DeepMind says it is the first time watermarked ai-designed proteins have been made and shown to work.

A parallel project with the Hie lab at Stanford and the Arc Institute used it to watermark a bacteriophage genome designed with the Evo 2 model, which worked in bacterial culture. A technical write-up of that work is still to come.

Why it matters

The companies that screen DNA synthesis orders can't currently tell an ai-designed sequence from a natural one. A watermark gives them a label to triage on, and keeps synthetic entries identifiable in public databases such as the Protein Data Bank, UniProt and GenBank.

DeepMind is clear that this isn't a defence against a determined adversary. Resistance to deliberate tampering is unsolved, and a missing watermark tells you nothing.