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5,818 results

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Page 1
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. Update in: Nat Chem Biol. 2024 Aug;20(8):974-980. doi: 10.1038/s41589-024-01632-2 PMID: 37662224 Free PMC article. Updated. Preprint.
Sentinel cells enable genetic detection of SARS-CoV-2 Spike protein.
Weinberg ZY, Hilburger CE, Kim M, Cao L, Khalid M, Elmes S, Diwanji D, Hernandez E, Lopez J, Schaefer K, Smith AM, Zhou F; QCRG Structural Biology Consortium; Kumar GR, Ott M, Baker D, El-Samad H. Weinberg ZY, et al. Among authors: baker d. bioRxiv [Preprint]. 2021 Apr 20:2021.04.20.440678. doi: 10.1101/2021.04.20.440678. bioRxiv. 2021. PMID: 33907743 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. Update in: Nat Biotechnol. 2022 Sep;40(9):1336-1340. doi: 10.1038/s41587-022-01280-8 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. Update in: Sci Transl Med. 2022 May 25;14(646):eabn1252. doi: 10.1126/scitranslmed.abn1252 PMID: 34268509 Free PMC article. Updated. Preprint.
Massively parallel protein-protein interaction measurement by sequencing (MP3-seq) enables rapid screening of protein heterodimers.
Baryshev A, La Fleur A, Groves B, Michel C, Baker D, Ljubetič A, Seelig G. Baryshev A, et al. Among authors: baker d. bioRxiv [Preprint]. 2023 Aug 16:2023.02.08.527770. doi: 10.1101/2023.02.08.527770. bioRxiv. 2023. Update in: Nat Chem Biol. 2024 Nov;20(11):1514-1523. doi: 10.1038/s41589-024-01718-x PMID: 36798377 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. 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.
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. Update in: Nature. 2024 Mar;627(8005):898-904. doi: 10.1038/s41586-024-07188-4 PMID: 37333359 Free PMC article. Updated. Preprint.
De novo design of modular protein hydrogels with programmable intra- and extracellular viscoelasticity.
Mout R, Bretherton RC, Decarreau J, Lee S, Edman NI, Ahlrichs M, Hsia Y, Sahtoe DD, Ueda G, Gregorio N, Sharma A, Schulman R, DeForest CA, Baker D. Mout R, et al. Among authors: baker d. bioRxiv [Preprint]. 2023 Jun 3:2023.06.02.543449. doi: 10.1101/2023.06.02.543449. bioRxiv. 2023. Update in: Proc Natl Acad Sci U S A. 2024 Feb 6;121(6):e2309457121. doi: 10.1073/pnas.2309457121 PMID: 37398067 Free PMC article. Updated. Preprint.
De novo design of diverse small molecule binders and sensors using Shape Complementary Pseudocycles.
An L, Said M, Tran L, Majumder S, Goreshnik I, Lee GR, Juergens D, Dauparas J, Anishchenko I, Coventry B, Bera AK, Kang A, Levine PM, Alvarez V, Pillai A, Norn C, Feldman D, Zorine D, Hicks DR, Li X, Sanchez MG, Vafeados DK, Salveson PJ, Vorobieva AA, Baker D. An L, et al. Among authors: baker d. bioRxiv [Preprint]. 2023 Dec 21:2023.12.20.572602. doi: 10.1101/2023.12.20.572602. bioRxiv. 2023. Update in: Science. 2024 Jul 19;385(6706):276-282. doi: 10.1126/science.adn3780 PMID: 38187589 Free PMC article. Updated. 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. Update in: Science. 2024 Jul 19;385(6706):282-288. doi: 10.1126/science.adn3796 PMID: 38187764 Free PMC article. Updated. Preprint.
5,818 results