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Improved protein binder design using β-pairing targeted RFdiffusion.

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Title: Improved protein binder design using β-pairing targeted RFdiffusion.
Authors: Sappington I; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA.; Graduate Program in Biological Physics, Structure and Design, University of Washington, Seattle, WA, USA., Toul M; Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.; Unit for Structural Biology, VIB Center for Inflammation Research, Ghent, Belgium., Lee DS; Institute for Protein Design, University of Washington, Seattle, WA, USA.; Department of Genome Sciences, University of Washington, Seattle, WA, USA., Robinson SA; Department of Chemistry, Stanford University, Stanford, CA, USA., Goreshnik I; Institute for Protein Design, University of Washington, Seattle, WA, USA.; Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA., McCurdy C; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA.; Graduate Program in Biological Physics, Structure and Design, University of Washington, Seattle, WA, USA.; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA., Chan TC; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA., Buchholz N; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA., Huang B; Institute for Protein Design, University of Washington, Seattle, WA, USA.; Department of Bioengineering, University of Washington, Seattle, WA, USA., Vafeados D; Institute for Protein Design, University of Washington, Seattle, WA, USA., Garcia-Sanchez M; Institute for Protein Design, University of Washington, Seattle, WA, USA., Roullier N; Institute for Protein Design, University of Washington, Seattle, WA, USA., Glögl M; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA., Kim CJ; Institute for Protein Design, University of Washington, Seattle, WA, USA.; Department of Chemistry, University of Minnesota, Minneapolis, MN, USA., Watson JL; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA., Torres SV; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA.; Graduate Program in Biological Physics, Structure and Design, University of Washington, Seattle, WA, USA., Verschueren KHG; Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.; Unit for Structural Biology, VIB Center for Inflammation Research, Ghent, Belgium., Verstraete K; Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.; Unit for Structural Biology, VIB Center for Inflammation Research, Ghent, Belgium., Hinck CS; Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA., Benard-Valle M; Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens, Lyngby, Denmark., 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., Sims JN; Institute for Protein Design, University of Washington, Seattle, WA, USA.; Molecular & Cellular Biology, Medical Scientist Training Program, University of Washington, Seattle, WA, USA., Ahn G; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA., Wang X; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA., Hinck AP; Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA., Jenkins TP; Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens, Lyngby, Denmark., Ruohola-Baker H; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA., Banik SM; Department of Chemistry, Stanford University, Stanford, CA, USA.; Sarafan ChEM-H, Stanford University, Stanford, CA, USA., Savvides SN; Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.; Unit for Structural Biology, VIB Center for Inflammation Research, Ghent, Belgium., 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 communications [Nat Commun] 2026 Jan 10; Vol. 17 (1), pp. 1101. Date of Electronic Publication: 2026 Jan 10.
Publication Type: Journal Article
Journal Info: Publisher: Nature Pub. Group Country of Publication: England NLM ID: 101528555 Publication Model: Electronic Cited Medium: Internet ISSN: 2041-1723 (Electronic) Linking ISSN: 20411723 NLM ISO Abbreviation: Nat Commun Subsets: MEDLINE
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  Data: <searchLink fieldCode="AU" term="%22Sappington+I%22">Sappington I</searchLink>; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA.; Graduate Program in Biological Physics, Structure and Design, University of Washington, Seattle, WA, USA.<br /><searchLink fieldCode="AU" term="%22Toul+M%22">Toul M</searchLink>; Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.; Unit for Structural Biology, VIB Center for Inflammation Research, Ghent, Belgium.<br /><searchLink fieldCode="AU" term="%22Lee+DS%22">Lee DS</searchLink>; Institute for Protein Design, University of Washington, Seattle, WA, USA.; Department of Genome Sciences, University of Washington, Seattle, WA, USA.<br /><searchLink fieldCode="AU" term="%22Robinson+SA%22">Robinson SA</searchLink>; Department of Chemistry, Stanford University, Stanford, CA, USA.<br /><searchLink fieldCode="AU" term="%22Goreshnik+I%22">Goreshnik I</searchLink>; 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="%22McCurdy+C%22">McCurdy C</searchLink>; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA.; Graduate Program in Biological Physics, Structure and Design, University of Washington, Seattle, WA, USA.; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA.<br /><searchLink fieldCode="AU" term="%22Chan+TC%22">Chan TC</searchLink>; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA.<br /><searchLink fieldCode="AU" term="%22Buchholz+N%22">Buchholz N</searchLink>; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA.<br /><searchLink fieldCode="AU" term="%22Huang+B%22">Huang B</searchLink>; 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Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA.<br /><searchLink fieldCode="AU" term="%22Torres+SV%22">Torres SV</searchLink>; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA.; Graduate Program in Biological Physics, Structure and Design, University of Washington, Seattle, WA, USA.<br /><searchLink fieldCode="AU" term="%22Verschueren+KHG%22">Verschueren KHG</searchLink>; Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.; Unit for Structural Biology, VIB Center for Inflammation Research, Ghent, Belgium.<br /><searchLink fieldCode="AU" term="%22Verstraete+K%22">Verstraete K</searchLink>; Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.; Unit for Structural Biology, VIB Center for Inflammation Research, Ghent, Belgium.<br /><searchLink fieldCode="AU" term="%22Hinck+CS%22">Hinck CS</searchLink>; Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.<br /><searchLink fieldCode="AU" term="%22Benard-Valle+M%22">Benard-Valle M</searchLink>; Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens, Lyngby, Denmark.<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="%22Sims+JN%22">Sims JN</searchLink>; Institute for Protein Design, University of Washington, Seattle, WA, USA.; Molecular & Cellular Biology, Medical Scientist Training Program, University of Washington, Seattle, WA, USA.<br /><searchLink fieldCode="AU" term="%22Ahn+G%22">Ahn G</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="%22Wang+X%22">Wang X</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="%22Hinck+AP%22">Hinck AP</searchLink>; Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.<br /><searchLink fieldCode="AU" term="%22Jenkins+TP%22">Jenkins TP</searchLink>; Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens, Lyngby, Denmark.<br /><searchLink fieldCode="AU" term="%22Ruohola-Baker+H%22">Ruohola-Baker H</searchLink>; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA.<br /><searchLink fieldCode="AU" term="%22Banik+SM%22">Banik SM</searchLink>; Department of Chemistry, Stanford University, Stanford, CA, USA.; 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