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Page 1
Accurate computational design of three-dimensional protein crystals.
Li Z, Wang S, Nattermann U, Bera AK, Borst AJ, Yaman MY, Bick MJ, Yang EC, Sheffler W, Lee B, Seifert S, Hura GL, Nguyen H, Kang A, Dalal R, Lubner JM, Hsia Y, Haddox H, Courbet A, Dowling Q, Miranda M, Favor A, Etemadi A, Edman NI, Yang W, Weidle C, Sankaran B, Negahdari B, Ross MB, Ginger DS, Baker D. Li Z, et al. Among authors: miranda m. Nat Mater. 2023 Dec;22(12):1556-1563. doi: 10.1038/s41563-023-01683-1. Epub 2023 Oct 16. Nat Mater. 2023. PMID: 37845322
De novo design of modular and tunable protein biosensors.
Quijano-Rubio A, Yeh HW, Park J, Lee H, Langan RA, Boyken SE, Lajoie MJ, Cao L, Chow CM, Miranda MC, Wi J, Hong HJ, Stewart L, Oh BH, Baker D. Quijano-Rubio A, et al. Among authors: miranda mc. Nature. 2021 Mar;591(7850):482-487. doi: 10.1038/s41586-021-03258-z. Epub 2021 Jan 27. Nature. 2021. PMID: 33503651 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: miranda m. 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.
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: miranda mc. 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.
Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies.
Edman NI, Redler RL, Phal A, Schlichthaerle T, Srivatsan SR, Etemadi A, An SJ, Favor A, Ehnes D, Li Z, Praetorius F, Gordon M, Yang W, Coventry B, Hicks DR, Cao L, Bethel N, Heine P, Murray A, Gerben S, Carter L, Miranda M, Negahdari B, Lee S, Trapnell C, Stewart L, Ekiert DC, Schlessinger J, Shendure J, Bhabha G, Ruohola-Baker H, Baker D. Edman NI, et al. Among authors: miranda m. bioRxiv [Preprint]. 2023 Mar 15:2023.03.14.532666. doi: 10.1101/2023.03.14.532666. bioRxiv. 2023. Update in: Cell. 2024 Jul 11;187(14):3726-3740.e43. doi: 10.1016/j.cell.2024.05.025. PMID: 36993355 Free PMC article. Updated. Preprint.
Computational design of non-porous, pH-responsive antibody nanoparticles.
Yang EC, Divine R, Miranda MC, Borst AJ, Sheffler W, Zhang JZ, Decarreau J, Saragovi A, Abedi M, Goldbach N, Ahlrichs M, Dobbins C, Hand A, Cheng S, Lamb M, Levine PM, Chan S, Skotheim R, Fallas J, Ueda G, Lubner J, Somiya M, Khmelinskaia A, King NP, Baker D. Yang EC, et al. Among authors: miranda mc. bioRxiv [Preprint]. 2023 Apr 18:2023.04.17.537263. doi: 10.1101/2023.04.17.537263. bioRxiv. 2023. Update in: Nat Struct Mol Biol. 2024 Sep;31(9):1404-1412. doi: 10.1038/s41594-024-01288-5. PMID: 37131615 Free PMC article. Updated. Preprint.
De novo design of highly selective miniprotein inhibitors of integrins αvβ6 and αvβ8.
Roy A, Shi L, Chang A, Dong X, Fernandez A, Kraft JC, Li J, Le VQ, Winegar RV, Cherf GM, Slocum D, Daniel Poulson P, Casper GE, Vallecillo-Zúniga ML, Valdoz JC, Miranda MC, Bai H, Kipnis Y, Olshefsky A, Priya T, Carter L, Ravichandran R, Chow CM, Johnson MR, Cheng S, Smith M, Overed-Sayer C, Finch DK, Lowe D, Bera AK, Matute-Bello G, Birkland TP, DiMaio F, Raghu G, Cochran JR, Stewart LJ, Campbell MG, Van Ry PM, Springer T, Baker D. Roy A, et al. Among authors: miranda mc. bioRxiv [Preprint]. 2023 Jun 12:2023.06.12.544624. doi: 10.1101/2023.06.12.544624. bioRxiv. 2023. Update in: Nat Commun. 2023 Sep 13;14(1):5660. doi: 10.1038/s41467-023-41272-z. PMID: 37398153 Free PMC article. Updated. Preprint.
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: miranda mc. 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.
De novo design of highly selective miniprotein inhibitors of integrins αvβ6 and αvβ8.
Roy A, Shi L, Chang A, Dong X, Fernandez A, Kraft JC, Li J, Le VQ, Winegar RV, Cherf GM, Slocum D, Poulson PD, Casper GE, Vallecillo-Zúniga ML, Valdoz JC, Miranda MC, Bai H, Kipnis Y, Olshefsky A, Priya T, Carter L, Ravichandran R, Chow CM, Johnson MR, Cheng S, Smith M, Overed-Sayer C, Finch DK, Lowe D, Bera AK, Matute-Bello G, Birkland TP, DiMaio F, Raghu G, Cochran JR, Stewart LJ, Campbell MG, Van Ry PM, Springer T, Baker D. Roy A, et al. Among authors: miranda mc. Nat Commun. 2023 Sep 13;14(1):5660. doi: 10.1038/s41467-023-41272-z. Nat Commun. 2023. PMID: 37704610 Free PMC article.
Computational design of non-porous pH-responsive antibody nanoparticles.
Yang EC, Divine R, Miranda MC, Borst AJ, Sheffler W, Zhang JZ, Decarreau J, Saragovi A, Abedi M, Goldbach N, Ahlrichs M, Dobbins C, Hand A, Cheng S, Lamb M, Levine PM, Chan S, Skotheim R, Fallas J, Ueda G, Lubner J, Somiya M, Khmelinskaia A, King NP, Baker D. Yang EC, et al. Among authors: miranda mc. Nat Struct Mol Biol. 2024 Sep;31(9):1404-1412. doi: 10.1038/s41594-024-01288-5. Epub 2024 May 9. Nat Struct Mol Biol. 2024. PMID: 38724718 Free PMC article.
2,980 results