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With serine hydrolases as a model system, we combined the generative capabilities of RFdiffusion with an ensemble generation method for assessing active site preorganization at each step in the reaction to design enzymes starting from minimal active site descriptions. Experimental characterization revealed catalytic efficiencies (\n                    <jats:italic>k<\/jats:italic>\n                    <jats:sub>cat<\/jats:sub>\n                    \/\n                    <jats:italic>K<\/jats:italic>\n                    <jats:sub>m<\/jats:sub>\n                    ) up to 2.2 \u00d7 10\n                    <jats:sup>5<\/jats:sup>\n                    M\n                    <jats:sup>\u22121<\/jats:sup>\n                    s\n                    <jats:sup>\u22121<\/jats:sup>\n                    and crystal structures that closely match the design models (C\u03b1 root mean square deviations &lt;1 angstrom). Selection for structural compatibility across the reaction coordinate enabled identification of new catalysts remove with five different folds distinct from those of natural serine hydrolases. Our de novo approach provides insight into the geometric basis of catalysis and a roadmap for designing enzymes that catalyze multistep transformations.\n                  <\/jats:p>","DOI":"10.1126\/science.adu2454","type":"journal-article","created":{"date-parts":[[2025,2,13]],"date-time":"2025-02-13T13:59:41Z","timestamp":1739455181000},"update-policy":"https:\/\/doi.org\/10.34133\/aaas_crossmark","source":"Crossref","is-referenced-by-count":217,"title":["Computational design of serine hydrolases"],"prefix":"10.1126","volume":"388","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5903-3518","authenticated-orcid":true,"given":"Anna","family":"Lauko","sequence":"first","affiliation":[{"name":"Department of Biochemistry, University of Washington, Seattle, WA, USA."},{"name":"Institute for Protein Design, University of Washington, Seattle, WA, USA."},{"name":"Graduate Program in Biological Physics, Structure and Design, University of Washington, Seattle, WA, USA."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7557-7985","authenticated-orcid":true,"given":"Samuel J.","family":"Pellock","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, University of Washington, Seattle, WA, USA."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2773-9676","authenticated-orcid":true,"given":"Kiera H.","family":"Sumida","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, University of Washington, Seattle, WA, USA."},{"name":"Institute for Protein Design, University of Washington, Seattle, WA, USA."},{"name":"Department of Chemistry, University of Washington, Seattle, WA, USA."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3645-2044","authenticated-orcid":true,"given":"Ivan","family":"Anishchenko","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, University of Washington, Seattle, WA, USA."},{"name":"Institute for Protein Design, University of Washington, Seattle, WA, USA."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6425-8391","authenticated-orcid":true,"given":"David","family":"Juergens","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, University of Washington, Seattle, WA, USA."},{"name":"Institute for Protein Design, University of Washington, Seattle, WA, USA."},{"name":"Graduate Program in Molecular Engineering, University of Washington, Seattle, WA, USA."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-1247-8847","authenticated-orcid":true,"given":"Woody","family":"Ahern","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, University of Washington, Seattle, WA, USA."},{"name":"Institute for Protein Design, University of Washington, Seattle, WA, USA."},{"name":"Paul G. 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