SynthID Bio: watermarking AI-designed proteins while fine‑tuning AlphaFold 3
The authors introduce SynthID Bio, a family of watermarking methods that embeds imperceptible signatures into protein sequences and predicted 3D coordinates so the watermark is verifiable on synthesized proteins; in wet‑lab tests on three targets (VEGF‑A, SARS‑CoV‑2 RBD, PD‑L1) watermarked protein binders retained hit rates, binding affinities, and sequence diversity comparable to unwatermarked designs. For folding, the approach fine‑tunes part of AlphaFold 3’s diffusion network to make predicted coordinates carry a detectable signature while preserving prediction accuracy and structural feature distributions.