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Page 1
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: goreshnik i. bioRxiv [Preprint]. 2023 Dec 21:2023.12.20.572602. doi: 10.1101/2023.12.20.572602. bioRxiv. 2023. PMID: 38187589 Free PMC article. Preprint.
De novo design of picomolar SARS-CoV-2 miniprotein inhibitors.
Cao L, Goreshnik I, Coventry B, Case JB, Miller L, Kozodoy L, Chen RE, Carter L, Walls L, Park YJ, Stewart L, Diamond M, Veesler D, Baker D. Cao L, et al. Among authors: goreshnik i. bioRxiv [Preprint]. 2020 Aug 3:2020.08.03.234914. doi: 10.1101/2020.08.03.234914. bioRxiv. 2020. PMID: 32793905 Free PMC article. Updated. Preprint.
Design of protein-binding proteins from the target structure alone.
Cao L, Coventry B, Goreshnik I, Huang B, Sheffler W, Park JS, Jude KM, Marković I, Kadam RU, Verschueren KHG, Verstraete K, Walsh STR, Bennett N, Phal A, Yang A, Kozodoy L, DeWitt M, Picton L, Miller L, Strauch EM, DeBouver ND, Pires A, Bera AK, Halabiya S, Hammerson B, Yang W, Bernard S, Stewart L, Wilson IA, Ruohola-Baker H, Schlessinger J, Lee S, Savvides SN, Garcia KC, Baker D. Cao L, et al. Among authors: goreshnik i. Nature. 2022 May;605(7910):551-560. doi: 10.1038/s41586-022-04654-9. Epub 2022 Mar 24. Nature. 2022. PMID: 35332283 Free PMC article.
De novo design of modular peptide-binding proteins by superhelical matching.
Wu K, Bai H, Chang YT, Redler R, McNally KE, Sheffler W, Brunette TJ, Hicks DR, Morgan TE, Stevens TJ, Broerman A, Goreshnik I, DeWitt M, Chow CM, Shen Y, Stewart L, Derivery E, Silva DA, Bhabha G, Ekiert DC, Baker D. Wu K, et al. Among authors: goreshnik i. Nature. 2023 Apr;616(7957):581-589. doi: 10.1038/s41586-023-05909-9. Epub 2023 Apr 5. Nature. 2023. PMID: 37020023 Free PMC article.
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: goreshnik i. Nat Commun. 2023 May 6;14(1):2625. doi: 10.1038/s41467-023-38328-5. Nat Commun. 2023. PMID: 37149653 Free PMC article.
Designed Endocytosis-Triggering Proteins mediate Targeted Degradation.
Huang B, Abedi M, Ahn G, Coventry B, Sappington I, Wang R, Schlichthaerle T, Zhang JZ, Wang Y, Goreshnik I, Chiu CW, Chazin-Gray A, Chan S, Gerben S, Murray A, Wang S, O'Neill J, Yeh R, Misquith A, Wolf A, Tomasovic LM, Piraner DI, Gonzalez MJD, Bennett NR, Venkatesh P, Satoe D, Ahlrichs M, Dobbins C, Yang W, Wang X, Vafeados D, Mout R, Shivaei S, Cao L, Carter L, Stewart L, Spangler JB, Bernardes GJL, Roybal KT, Greisen P Jr, Li X, Bertozzi C, Baker D. Huang B, et al. Among authors: goreshnik i. bioRxiv [Preprint]. 2023 Sep 20:2023.08.19.553321. doi: 10.1101/2023.08.19.553321. bioRxiv. 2023. PMID: 37781607 Free PMC article. Preprint.
Computational design of sequence-specific DNA-binding proteins.
Glasscock CJ, Pecoraro R, McHugh R, Doyle LA, Chen W, Boivin O, Lonnquist B, Na E, Politanska Y, Haddox HK, Cox D, Norn C, Coventry B, Goreshnik I, Vafeados D, Lee GR, Gordan R, Stoddard BL, DiMaio F, Baker D. Glasscock CJ, et al. Among authors: goreshnik i. bioRxiv [Preprint]. 2023 Sep 21:2023.09.20.558720. doi: 10.1101/2023.09.20.558720. bioRxiv. 2023. PMID: 37790440 Free PMC article. 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. Among authors: goreshnik i. bioRxiv [Preprint]. 2023 Nov 2:2023.11.01.565201. doi: 10.1101/2023.11.01.565201. bioRxiv. 2023. PMID: 37961294 Free PMC article. Preprint.
24 results