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Atom-level enzyme active site scaffolding using RFdiffusion2.

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Title: Atom-level enzyme active site scaffolding using RFdiffusion2.
Authors: Ahern W; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA.; Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA., Yim J; Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA.; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA., Tischer D; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA., Salike S; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA., Woodbury SM; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA., Kim D; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA., Kalvet I; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA.; Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA., Kipnis Y; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA.; Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA., Coventry B; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA.; Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA., Altae-Tran HR; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA., Bauer MS; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA., Barzilay R; Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA.; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA., Jaakkola TS; Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA.; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA., Krishna R; Department of Biochemistry, University of Washington, Seattle, WA, USA. rohith@uw.edu.; Institute for Protein Design, University of Washington, Seattle, WA, USA. rohith@uw.edu., Baker D; Department of Biochemistry, University of Washington, Seattle, WA, USA. dabaker@uw.edu.; Institute for Protein Design, University of Washington, Seattle, WA, USA. dabaker@uw.edu.; Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA. dabaker@uw.edu.
Source: Nature methods [Nat Methods] 2026 Jan; Vol. 23 (1), pp. 96-105. Date of Electronic Publication: 2025 Dec 03.
Publication Type: Journal Article
Journal Info: Publisher: Nature Pub. Group Country of Publication: United States NLM ID: 101215604 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1548-7105 (Electronic) Linking ISSN: 15487091 NLM ISO Abbreviation: Nat Methods Subsets: MEDLINE
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  Data: <searchLink fieldCode="AU" term="%22Ahern+W%22">Ahern W</searchLink>; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA.; Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA.<br /><searchLink fieldCode="AU" term="%22Yim+J%22">Yim J</searchLink>; Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA.; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA.<br /><searchLink fieldCode="AU" term="%22Tischer+D%22">Tischer D</searchLink>; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA.<br /><searchLink fieldCode="AU" term="%22Salike+S%22">Salike S</searchLink>; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA.<br /><searchLink fieldCode="AU" term="%22Woodbury+SM%22">Woodbury SM</searchLink>; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA.<br /><searchLink fieldCode="AU" term="%22Kim+D%22">Kim D</searchLink>; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA.<br /><searchLink fieldCode="AU" term="%22Kalvet+I%22">Kalvet I</searchLink>; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA.; Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.<br /><searchLink fieldCode="AU" term="%22Kipnis+Y%22">Kipnis Y</searchLink>; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA.; Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.<br /><searchLink fieldCode="AU" term="%22Coventry+B%22">Coventry B</searchLink>; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA.; Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.<br /><searchLink fieldCode="AU" term="%22Altae-Tran+HR%22">Altae-Tran HR</searchLink>; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA.<br /><searchLink fieldCode="AU" term="%22Bauer+MS%22">Bauer MS</searchLink>; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA.<br /><searchLink fieldCode="AU" term="%22Barzilay+R%22">Barzilay R</searchLink>; Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA.; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA.<br /><searchLink fieldCode="AU" term="%22Jaakkola+TS%22">Jaakkola TS</searchLink>; Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA.; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA.<br /><searchLink fieldCode="AU" term="%22Krishna+R%22">Krishna R</searchLink>; Department of Biochemistry, University of Washington, Seattle, WA, USA. rohith@uw.edu.; Institute for Protein Design, University of Washington, Seattle, WA, USA. rohith@uw.edu.<br /><searchLink fieldCode="AU" term="%22Baker+D%22">Baker D</searchLink>; Department of Biochemistry, University of Washington, Seattle, WA, USA. dabaker@uw.edu.; Institute for Protein Design, University of Washington, Seattle, WA, USA. dabaker@uw.edu.; Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA. dabaker@uw.edu.
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