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231 results

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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: bera ak. 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.
Design of Diverse Asymmetric Pockets in De Novo Homo-oligomeric Proteins.
Gerben SR, Borst AJ, Hicks DR, Moczygemba I, Feldman D, Coventry B, Yang W, Bera AK, Miranda M, Kang A, Nguyen H, Baker D. Gerben SR, et al. Among authors: bera ak. Biochemistry. 2023 Jan 17;62(2):358-368. doi: 10.1021/acs.biochem.2c00497. Epub 2023 Jan 10. Biochemistry. 2023. PMID: 36627259 Free PMC article.
Cyclic peptide structure prediction and design using AlphaFold.
Rettie SA, Campbell KV, Bera AK, Kang A, Kozlov S, De La Cruz J, Adebomi V, Zhou G, DiMaio F, Ovchinnikov S, Bhardwaj G. Rettie SA, et al. Among authors: bera ak. bioRxiv [Preprint]. 2023 Feb 26:2023.02.25.529956. doi: 10.1101/2023.02.25.529956. bioRxiv. 2023. PMID: 36865323 Free PMC article. 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: bera ak. 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 designed ice-binding proteins from twist-constrained helices.
de Haas RJ, Tas RP, van den Broek D, Zheng C, Nguyen H, Kang A, Bera AK, King NP, Voets IK, de Vries R. de Haas RJ, et al. Among authors: bera ak. Proc Natl Acad Sci U S A. 2023 Jul 4;120(27):e2220380120. doi: 10.1073/pnas.2220380120. Epub 2023 Jun 26. Proc Natl Acad Sci U S A. 2023. PMID: 37364125 Free PMC article.
De novo design of highly selective miniprotein inhibitors of integrins αvβ6 and αvβ8.
Roy A, Shi L, Chang A, Dong X, Fernandez A, Kraft JC, Li J, Le VQ, Winegar RV, Cherf GM, Slocum D, Daniel Poulson P, Casper GE, Vallecillo-Zúniga ML, Valdoz JC, Miranda MC, Bai H, Kipnis Y, Olshefsky A, Priya T, Carter L, Ravichandran R, Chow CM, Johnson MR, Cheng S, Smith M, Overed-Sayer C, Finch DK, Lowe D, Bera AK, Matute-Bello G, Birkland TP, DiMaio F, Raghu G, Cochran JR, Stewart LJ, Campbell MG, Van Ry PM, Springer T, Baker D. Roy A, et al. Among authors: bera ak. bioRxiv [Preprint]. 2023 Jun 12:2023.06.12.544624. doi: 10.1101/2023.06.12.544624. bioRxiv. 2023. PMID: 37398153 Free PMC article. Updated. 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. 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: bera ak. bioRxiv [Preprint]. 2023 Dec 20:2023.12.20.572500. doi: 10.1101/2023.12.20.572500. bioRxiv. 2023. PMID: 38187764 Free PMC article. Preprint.
231 results