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Tracking and establishing the provenance of AI-generated protein sequences and structures is becoming increasingly important to tackle a range of emerging challenges, including biosecurity and concerns about information veracity\n                    <jats:sup>2\u20134<\/jats:sup>\n                    . Here we introduce SynthIDBio, a family of methods for watermarking protein sequences and structures to establish the provenance of those generated with AI. SynthIDBio-sequence actively embeds a watermark into protein sequences while preserving function. We demonstrate this by creating watermarked, functional designed protein binders with binding affinity comparable with non-watermarked counterparts and near-perfect watermark detection accuracy. Furthermore, SynthIDBio-structure, a fine-tuned AlphaFold3 model, embeds an imperceptible watermark into biomolecular structures. Our work is a proof-of-concept that function-preserving biological watermarking is feasible, introducing a potential tool for provenance in the rapidly expanding era of AI-driven biological engineering.\n                  <\/jats:p>","DOI":"10.1038\/s41586-026-10965-y","type":"journal-article","created":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T15:03:57Z","timestamp":1790780637000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Function-preserving watermarking of AI-generated proteins"],"prefix":"10.1038","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6286-1805","authenticated-orcid":false,"given":"David","family":"Stutz","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexander I.","family":"Cowen-Rivers","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guillermo","family":"Ortiz-Jimenez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6522-138X","authenticated-orcid":false,"given":"Jeremy","family":"Ratcliff","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vinicius","family":"Zambaldi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4314-0778","authenticated-orcid":false,"given":"Lindsay","family":"Willmore","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-3496-6952","authenticated-orcid":false,"given":"Josh","family":"Abramson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Harshnira","family":"Patani","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0007-8709-5709","authenticated-orcid":false,"given":"Christina","family":"Kouridi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Florian","family":"Stimberg","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mel","family":"Vecerik","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alex","family":"Chu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sukhdeep","family":"Singh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0007-4937-9903","authenticated-orcid":false,"given":"Sumanth","family":"Dathathri","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eliseo","family":"Papa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Valentin","family":"De Bortoli","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Arnaud","family":"Doucet","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2812-9917","authenticated-orcid":false,"given":"Demis","family":"Hassabis","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jue","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sven","family":"Gowal","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7466-7997","authenticated-orcid":false,"given":"Pushmeet","family":"Kohli","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,9,30]]},"reference":[{"key":"10965_CR1","doi-asserted-by":"publisher","first-page":"102794","DOI":"10.1016\/j.sbi.2024.102794","volume":"86","author":"A Winnifrith","year":"2024","unstructured":"Winnifrith, A., Outeiral, C. & Hie, B. 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