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Local structural flexibility drives oligomorphism in computationally designed protein assemblies.
Khmelinskaia A, Bethel NP, Fatehi F, Antanasijevic A, Borst AJ, Lai SH, Wang JYJ, Mallik BB, Miranda MC, Watkins AM, Ogohara C, Caldwell S, Wu M, Heck AJR, Veesler D, Ward AB, Baker D, Twarock R, King NP. Khmelinskaia A, et al. Among authors: baker d. bioRxiv [Preprint]. 2023 Oct 19:2023.10.18.562842. doi: 10.1101/2023.10.18.562842. bioRxiv. 2023. PMID: 37905007 Free PMC article. Preprint.
Detection of antibodies neutralizing historical and emerging SARS-CoV-2 strains using a thermodynamically coupled de novo biosensor system.
Zhang JZ, Yeh HW, Walls AC, Wicky BIM, Sprouse K, VanBlargan LA, Treger R, Quijano-Rubio A, Pham MN, Kraft JC, Haydon IC, Yang W, DeWitt M, Chow C, Carter L, Wener MH, Stewart L, Veesler D, Diamond MS, Baker D. Zhang JZ, et al. Among authors: baker d. bioRxiv [Preprint]. 2021 Jun 22:2021.06.22.449355. doi: 10.1101/2021.06.22.449355. bioRxiv. 2021. PMID: 34189528 Free PMC article. Updated. Preprint.
Multivalent designed proteins protect against SARS-CoV-2 variants of concern.
Hunt AC, Case JB, Park YJ, Cao L, Wu K, Walls AC, Liu Z, Bowen JE, Yeh HW, Saini S, Helms L, Zhao YT, Hsiang TY, Starr TN, Goreshnik I, Kozodoy L, Carter L, Ravichandran R, Green LB, Matochko WL, Thomson CA, Vögeli B, Krüger-Gericke A, VanBlargan LA, Chen RE, Ying B, Bailey AL, Kafai NM, Boyken S, Ljubetič A, Edman N, Ueda G, Chow C, Addetia A, Panpradist N, Gale M Jr, Freedman BS, Lutz BR, Bloom JD, Ruohola-Baker H, Whelan SPJ, Stewart L, Diamond MS, Veesler D, Jewett MC, Baker D. Hunt AC, et al. Among authors: baker d. bioRxiv [Preprint]. 2021 Jul 7:2021.07.07.451375. doi: 10.1101/2021.07.07.451375. bioRxiv. 2021. PMID: 34268509 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: baker d. bioRxiv [Preprint]. 2023 Apr 18:2023.04.17.537263. doi: 10.1101/2023.04.17.537263. bioRxiv. 2023. PMID: 37131615 Free PMC article. Updated. Preprint.
Blueprinting expandable nanomaterials with standardized protein building blocks.
Huddy TF, Hsia Y, Kibler RD, Xu J, Bethel N, Nagarajan D, Redler R, Leung PJY, Courbet A, Yang EC, Bera AK, Coudray N, Calise SJ, Davila-Hernandez FA, Weidle C, Han HL, Li Z, McHugh R, Reggiano G, Kang A, Sankaran B, Dickinson MS, Coventry B, Brunette TJ, Liu Y, Dauparas J, Borst AJ, Ekiert D, Kollman JM, Bhabha G, Baker D. Huddy TF, et al. Among authors: baker d. bioRxiv [Preprint]. 2023 Jun 9:2023.06.09.544258. doi: 10.1101/2023.06.09.544258. bioRxiv. 2023. PMID: 37333359 Free PMC article. Updated. Preprint.
De novo design of buttressed loops for sculpting protein functions.
Jiang H, Jude KM, Wu K, Fallas J, Ueda G, Brunette TJ, Hicks D, Pyles H, Yang A, Carter L, Lamb M, Li X, Levine PM, Stewart L, Garcia KC, Baker D. Jiang H, et al. Among authors: baker d. bioRxiv [Preprint]. 2023 Aug 23:2023.08.22.554384. doi: 10.1101/2023.08.22.554384. bioRxiv. 2023. PMID: 37662224 Free PMC article. Preprint.
Small-molecule binding and sensing with a designed protein family.
Lee GR, Pellock SJ, Norn C, Tischer D, Dauparas J, Anischenko I, Mercer JAM, Kang A, Bera A, Nguyen H, Goreshnik I, Vafeados D, Roullier N, Han HL, Coventry B, Haddox HK, Liu DR, Yeh AH, Baker D. Lee GR, et al. Among authors: baker d. bioRxiv [Preprint]. 2023 Nov 2:2023.11.01.565201. doi: 10.1101/2023.11.01.565201. bioRxiv. 2023. PMID: 37961294 Free PMC article. Preprint.
Sculpting conducting nanopore size and shape through de novo protein design.
Berhanu S, Majumder S, Müntener T, Whitehouse J, Berner C, Bera AK, Kang A, Liang B, Khan GN, Sankaran B, Tamm LK, Brockwell DJ, Hiller S, Radford SE, Baker D, Vorobieva AA. Berhanu S, et al. Among authors: baker d. bioRxiv [Preprint]. 2023 Dec 20:2023.12.20.572500. doi: 10.1101/2023.12.20.572500. bioRxiv. 2023. PMID: 38187764 Free PMC article. Preprint.
Computational design of soluble functional analogues of integral membrane proteins.
Goverde CA, Pacesa M, Goldbach N, Dornfeld LJ, Balbi PEM, Georgeon S, Rosset S, Kapoor S, Choudhury J, Dauparas J, Schellhaas C, Kozlov S, Baker D, Ovchinnikov S, Vecchio AJ, Correia BE. Goverde CA, et al. Among authors: baker d. bioRxiv [Preprint]. 2024 Mar 7:2023.05.09.540044. doi: 10.1101/2023.05.09.540044. bioRxiv. 2024. PMID: 38496615 Free PMC article. Preprint.
5,657 results