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Page 1
Computational design of bifaceted protein nanomaterials.
Rankovic S, Carr KD, Decarreau J, Skotheim R, Kibler RD, Ols S, Lee S, Chun JH, Tooley MR, Dauparas J, Eisenach HE, Glögl M, Weidle C, Borst AJ, Baker D, King NP. Rankovic S, et al. Among authors: baker d. bioRxiv [Preprint]. 2024 Dec 21:2024.10.18.619149. doi: 10.1101/2024.10.18.619149. bioRxiv. 2024. PMID: 39484564 Free PMC article. Preprint.
Designed proteins assemble antibodies into modular nanocages.
Divine R, Dang HV, Ueda G, Fallas JA, Vulovic I, Sheffler W, Saini S, Zhao YT, Raj IX, Morawski PA, Jennewein MF, Homad LJ, Wan YH, Tooley MR, Seeger F, Etemadi A, Fahning ML, Lazarovits J, Roederer A, Walls AC, Stewart L, Mazloomi M, King NP, Campbell DJ, McGuire AT, Stamatatos L, Ruohola-Baker H, Mathieu J, Veesler D, Baker D. Divine R, et al. Among authors: baker d. bioRxiv [Preprint]. 2020 Dec 1:2020.12.01.406611. doi: 10.1101/2020.12.01.406611. bioRxiv. 2020. Update in: Science. 2021 Apr 2;372(6537):eabd9994. doi: 10.1126/science.abd9994 PMID: 33299994 Free PMC article. Updated. Preprint.
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: baker d. 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.
Top-down design of protein architectures with reinforcement learning.
Lutz ID, Wang S, Norn C, Courbet A, Borst AJ, Zhao YT, Dosey A, Cao L, Xu J, Leaf EM, Treichel C, Litvicov P, Li Z, Goodson AD, Rivera-Sánchez P, Bratovianu AM, Baek M, King NP, Ruohola-Baker H, Baker D. Lutz ID, et al. Among authors: baker d. Science. 2023 Apr 21;380(6642):266-273. doi: 10.1126/science.adf6591. Epub 2023 Apr 20. Science. 2023. PMID: 37079676
Improving de novo protein binder design with deep learning.
Bennett NR, Coventry B, Goreshnik I, Huang B, Allen A, Vafeados D, Peng YP, Dauparas J, Baek M, Stewart L, DiMaio F, De Munck S, Savvides SN, Baker D. Bennett NR, et al. Among authors: baker d. Nat Commun. 2023 May 6;14(1):2625. doi: 10.1038/s41467-023-38328-5. Nat Commun. 2023. PMID: 37149653 Free PMC article.
Fast and versatile sequence-independent protein docking for nanomaterials design using RPXDock.
Sheffler W, Yang EC, Dowling Q, Hsia Y, Fries CN, Stanislaw J, Langowski MD, Brandys M, Li Z, Skotheim R, Borst AJ, Khmelinskaia A, King NP, Baker D. Sheffler W, et al. Among authors: baker d. PLoS Comput Biol. 2023 May 22;19(5):e1010680. doi: 10.1371/journal.pcbi.1010680. eCollection 2023 May. PLoS Comput Biol. 2023. PMID: 37216343 Free PMC article.
5,818 results