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Page 1
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.
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.
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. Update in: Nat Commun. 2023 Sep 13;14(1):5660. doi: 10.1038/s41467-023-41272-z PMID: 37398153 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: bera ak. 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.
Improving Protein Expression, Stability, and Function with ProteinMPNN.
Sumida KH, Núñez-Franco R, Kalvet I, Pellock SJ, Wicky BIM, Milles LF, Dauparas J, Wang J, Kipnis Y, Jameson N, Kang A, De La Cruz J, Sankaran B, Bera AK, Jiménez-Osés G, Baker D. Sumida KH, et al. Among authors: bera ak. J Am Chem Soc. 2024 Jan 24;146(3):2054-2061. doi: 10.1021/jacs.3c10941. Epub 2024 Jan 9. J Am Chem Soc. 2024. PMID: 38194293 Free PMC article.
Rapid and automated design of two-component protein nanomaterials using ProteinMPNN.
de Haas RJ, Brunette N, Goodson A, Dauparas J, Yi SY, Yang EC, Dowling Q, Nguyen H, Kang A, Bera AK, Sankaran B, de Vries R, Baker D, King NP. de Haas RJ, et al. Among authors: bera ak. Proc Natl Acad Sci U S A. 2024 Mar 26;121(13):e2314646121. doi: 10.1073/pnas.2314646121. Epub 2024 Mar 19. Proc Natl Acad Sci U S A. 2024. PMID: 38502697 Free PMC article.
258 results