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Page 1
Atomically accurate de novo design of single-domain antibodies.
Bennett NR, Watson JL, Ragotte RJ, Borst AJ, See DL, Weidle C, Biswas R, Shrock EL, Leung PJY, Huang B, Goreshnik I, Ault R, Carr KD, Singer B, Criswell C, Vafeados D, Sanchez MG, Kim HM, Torres SV, Chan S, Baker D. Bennett NR, et al. Among authors: leung pjy. bioRxiv [Preprint]. 2024 Mar 18:2024.03.14.585103. doi: 10.1101/2024.03.14.585103. bioRxiv. 2024. PMID: 38562682 Free PMC article. Preprint.
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: leung pjy. Science. 2022 Oct 7;378(6615):49-56. doi: 10.1126/science.add2187. Epub 2022 Sep 15. Science. 2022. PMID: 36108050 Free PMC article.
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: leung pjy. 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 high-affinity binders of bioactive helical peptides.
Vázquez Torres S, Leung PJY, Venkatesh P, Lutz ID, Hink F, Huynh HH, Becker J, Yeh AH, Juergens D, Bennett NR, Hoofnagle AN, Huang E, MacCoss MJ, Expòsit M, Lee GR, Bera AK, Kang A, De La Cruz J, Levine PM, Li X, Lamb M, Gerben SR, Murray A, Heine P, Korkmaz EN, Nivala J, Stewart L, Watson JL, Rogers JM, Baker D. Vázquez Torres S, et al. Among authors: leung pjy. Nature. 2024 Feb;626(7998):435-442. doi: 10.1038/s41586-023-06953-1. Epub 2023 Dec 18. Nature. 2024. PMID: 38109936 Free PMC article.
De novo design of allosterically switchable protein assemblies.
Pillai A, Idris A, Philomin A, Weidle C, Skotheim R, Leung PJY, Broerman A, Demakis C, Borst AJ, Praetorius F, Baker D. Pillai A, et al. Among authors: leung pjy. Nature. 2024 Aug;632(8026):911-920. doi: 10.1038/s41586-024-07813-2. Epub 2024 Aug 14. Nature. 2024. PMID: 39143214 Free PMC article.
Blueprinting extendable nanomaterials with standardized protein blocks.
Huddy TF, Hsia Y, Kibler RD, Xu J, Bethel N, Nagarajan D, Redler R, Leung PJY, Weidle C, Courbet A, Yang EC, Bera AK, Coudray N, Calise SJ, Davila-Hernandez FA, Han HL, Carr KD, 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: leung pjy. Nature. 2024 Mar;627(8005):898-904. doi: 10.1038/s41586-024-07188-4. Epub 2024 Mar 13. Nature. 2024. PMID: 38480887 Free PMC article.
Design of stimulus-responsive two-state hinge proteins.
Praetorius F, Leung PJY, Tessmer MH, Broerman A, Demakis C, Dishman AF, Pillai A, Idris A, Juergens D, Dauparas J, Li X, Levine PM, Lamb M, Ballard RK, Gerben SR, Nguyen H, Kang A, Sankaran B, Bera AK, Volkman BF, Nivala J, Stoll S, Baker D. Praetorius F, et al. Among authors: leung pjy. Science. 2023 Aug 18;381(6659):754-760. doi: 10.1126/science.adg7731. Epub 2023 Aug 17. Science. 2023. PMID: 37590357 Free PMC article.