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Protein sequence design by conformational landscape optimization.
Norn C, Wicky BIM, Juergens D, Liu S, Kim D, Tischer D, Koepnick B, Anishchenko I; Foldit Players; Baker D, Ovchinnikov S. Norn C, et al. Proc Natl Acad Sci U S A. 2021 Mar 16;118(11):e2017228118. doi: 10.1073/pnas.2017228118. Proc Natl Acad Sci U S A. 2021. PMID: 33712545 Free PMC article.
Scaffolding protein functional sites using deep learning.
Wang J, Lisanza S, Juergens D, Tischer D, Watson JL, Castro KM, Ragotte R, Saragovi A, Milles LF, Baek M, Anishchenko I, Yang W, Hicks DR, Expòsit M, Schlichthaerle T, Chun JH, Dauparas J, Bennett N, Wicky BIM, Muenks A, DiMaio F, Correia B, Ovchinnikov S, Baker D. Wang J, et al. Among authors: wicky bim. Science. 2022 Jul 22;377(6604):387-394. doi: 10.1126/science.abn2100. Epub 2022 Jul 21. Science. 2022. PMID: 35862514 Free PMC article.
Robust deep learning-based protein sequence design using ProteinMPNN.
Dauparas J, Anishchenko I, Bennett N, Bai H, Ragotte RJ, Milles LF, Wicky BIM, Courbet A, de Haas RJ, Bethel N, Leung PJY, Huddy TF, Pellock S, Tischer D, Chan F, Koepnick B, Nguyen H, Kang A, Sankaran B, Bera AK, King NP, Baker D. Dauparas J, et al. Among authors: wicky bim. Science. 2022 Oct 7;378(6615):49-56. doi: 10.1126/science.add2187. Epub 2022 Sep 15. Science. 2022. PMID: 36108050 Free PMC article.
Reconfigurable asymmetric protein assemblies through implicit negative design.
Sahtoe DD, Praetorius F, Courbet A, Hsia Y, Wicky BIM, Edman NI, Miller LM, Timmermans BJR, Decarreau J, Morris HM, Kang A, Bera AK, Baker D. Sahtoe DD, et al. Among authors: wicky bim. Science. 2022 Jan 21;375(6578):eabj7662. doi: 10.1126/science.abj7662. Epub 2022 Jan 21. Science. 2022. PMID: 35050655 Free PMC article.
Hallucinating symmetric protein assemblies.
Wicky BIM, Milles LF, Courbet A, Ragotte RJ, Dauparas J, Kinfu E, Tipps S, Kibler RD, Baek M, DiMaio F, Li X, Carter L, Kang A, Nguyen H, Bera AK, Baker D. Wicky BIM, et al. Science. 2022 Oct 7;378(6615):56-61. doi: 10.1126/science.add1964. Epub 2022 Sep 15. Science. 2022. PMID: 36108048 Free PMC article.
De novo design of protein logic gates.
Chen Z, Kibler RD, Hunt A, Busch F, Pearl J, Jia M, VanAernum ZL, Wicky BIM, Dods G, Liao H, Wilken MS, Ciarlo C, Green S, El-Samad H, Stamatoyannopoulos J, Wysocki VH, Jewett MC, Boyken SE, Baker D. Chen Z, et al. Science. 2020 Apr 3;368(6486):78-84. doi: 10.1126/science.aay2790. Science. 2020. PMID: 32241946 Free PMC article.
22 results