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Improving the secretion of designed protein assemblies through negative design of cryptic transmembrane domains.
Wang JYJ, Khmelinskaia A, Sheffler W, Miranda MC, Antanasijevic A, Borst AJ, Torres SV, Shu C, Hsia Y, Nattermann U, Ellis D, Walkey C, Ahlrichs M, Chan S, Kang A, Nguyen H, Sydeman C, Sankaran B, Wu M, Bera AK, Carter L, Fiala B, Murphy M, Baker D, Ward AB, King NP. Wang JYJ, et al. Among authors: nguyen h. Proc Natl Acad Sci U S A. 2023 Mar 14;120(11):e2214556120. doi: 10.1073/pnas.2214556120. Epub 2023 Mar 8. Proc Natl Acad Sci U S A. 2023. PMID: 36888664 Free PMC article.
Design of Diverse Asymmetric Pockets in De Novo Homo-oligomeric Proteins.
Gerben SR, Borst AJ, Hicks DR, Moczygemba I, Feldman D, Coventry B, Yang W, Bera AK, Miranda M, Kang A, Nguyen H, Baker D. Gerben SR, et al. Among authors: nguyen h. Biochemistry. 2023 Jan 17;62(2):358-368. doi: 10.1021/acs.biochem.2c00497. Epub 2023 Jan 10. Biochemistry. 2023. PMID: 36627259 Free PMC article.
De novo design of small beta barrel proteins.
Kim DE, Jensen DR, Feldman D, Tischer D, Saleem A, Chow CM, Li X, Carter L, Milles L, Nguyen H, Kang A, Bera AK, Peterson FC, Volkman BF, Ovchinnikov S, Baker D. Kim DE, et al. Among authors: nguyen h. Proc Natl Acad Sci U S A. 2023 Mar 14;120(11):e2207974120. doi: 10.1073/pnas.2207974120. Epub 2023 Mar 10. Proc Natl Acad Sci U S A. 2023. PMID: 36897987 Free PMC article.
De novo designed ice-binding proteins from twist-constrained helices.
de Haas RJ, Tas RP, van den Broek D, Zheng C, Nguyen H, Kang A, Bera AK, King NP, Voets IK, de Vries R. de Haas RJ, et al. Among authors: nguyen h. Proc Natl Acad Sci U S A. 2023 Jul 4;120(27):e2220380120. doi: 10.1073/pnas.2220380120. Epub 2023 Jun 26. Proc Natl Acad Sci U S A. 2023. PMID: 37364125 Free PMC article.
Rapid and automated design of two-component protein nanomaterials using ProteinMPNN.
de Haas RJ, Brunette N, Goodson A, Dauparas J, Yi SY, Yang EC, Dowling Q, Nguyen H, Kang A, Bera AK, Sankaran B, de Vries R, Baker D, King NP. de Haas RJ, et al. Among authors: nguyen h. bioRxiv [Preprint]. 2023 Aug 4:2023.08.04.551935. doi: 10.1101/2023.08.04.551935. bioRxiv. 2023. PMID: 37577478 Free PMC article. Updated. Preprint.
Design of stimulus-responsive two-state hinge proteins.
Praetorius F, Leung PJY, Tessmer MH, Broerman A, Demakis C, Dishman AF, Pillai A, Idris A, Juergens D, Dauparas J, Li X, Levine PM, Lamb M, Ballard RK, Gerben SR, Nguyen H, Kang A, Sankaran B, Bera AK, Volkman BF, Nivala J, Stoll S, Baker D. Praetorius F, et al. Among authors: nguyen h. Science. 2023 Aug 18;381(6659):754-760. doi: 10.1126/science.adg7731. Epub 2023 Aug 17. Science. 2023. PMID: 37590357 Free PMC article.
Precisely patterned nanofibres made from extendable protein multiplexes.
Bethel NP, Borst AJ, Parmeggiani F, Bick MJ, Brunette TJ, Nguyen H, Kang A, Bera AK, Carter L, Miranda MC, Kibler RD, Lamb M, Li X, Sankaran B, Baker D. Bethel NP, et al. Among authors: nguyen h. Nat Chem. 2023 Dec;15(12):1664-1671. doi: 10.1038/s41557-023-01314-x. Epub 2023 Sep 4. Nat Chem. 2023. PMID: 37667012 Free PMC article.
Hallucination of closed repeat proteins containing central pockets.
An L, Hicks DR, Zorine D, Dauparas J, Wicky BIM, Milles LF, Courbet A, Bera AK, Nguyen H, Kang A, Carter L, Baker D. An L, et al. Among authors: nguyen h. Nat Struct Mol Biol. 2023 Nov;30(11):1755-1760. doi: 10.1038/s41594-023-01112-6. Epub 2023 Sep 28. Nat Struct Mol Biol. 2023. PMID: 37770718 Free PMC article.
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