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De novo design of diverse small molecule binders and sensors using Shape Complementary Pseudocycles.
bioRxiv [Preprint]. 2023 Dec 21:2023.12.20.572602. doi: 10.1101/2023.12.20.572602.
bioRxiv. 2023.
PMID: 38187589
Free PMC article.
Preprint.
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.
Nat Commun. 2023 May 6;14(1):2625. doi: 10.1038/s41467-023-38328-5.
Nat Commun. 2023.
PMID: 37149653
Free PMC article.
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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.
bioRxiv [Preprint]. 2023 Sep 20:2023.08.19.553321. doi: 10.1101/2023.08.19.553321.
bioRxiv. 2023.
PMID: 37781607
Free PMC article.
Preprint.
Item in Clipboard
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.
bioRxiv [Preprint]. 2023 Sep 21:2023.09.20.558720. doi: 10.1101/2023.09.20.558720.
bioRxiv. 2023.
PMID: 37790440
Free PMC article.
Preprint.
Item in Clipboard
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.
Item in Clipboard
Generalized biomolecular modeling and design with RoseTTAFold All-Atom.
Krishna R, Wang J, Ahern W, Sturmfels P, Venkatesh P, Kalvet I, Lee GR, Morey-Burrows FS, Anishchenko I, Humphreys IR, McHugh R, Vafeados D, Li X, Sutherland GA, Hitchcock A, Hunter CN, Kang A, Brackenbrough E, Bera AK, Baek M, DiMaio F, Baker D.
Krishna R, et al.
Science. 2024 Apr 19;384(6693):eadl2528. doi: 10.1126/science.adl2528. Epub 2024 Apr 19.
Science. 2024.
PMID: 38452047
Free article.
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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.
bioRxiv [Preprint]. 2024 Mar 18:2024.03.14.585103. doi: 10.1101/2024.03.14.585103.
bioRxiv. 2024.
PMID: 38562682
Free PMC article.
Preprint.
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Binding profiles for 954 Drosophila and C. elegans transcription factors reveal tissue specific regulatory relationships.
Kudron M, Gevirtzman L, Victorsen A, Lear BC, Gao J, Xu J, Samanta S, Frink E, Tran-Pearson A, Huynh C, Vafeados D, Hammonds A, Fisher W, Wall M, Wesseling G, Hernandez V, Lin Z, Kasparian M, White K, Allada R, Gerstein M, Hillier L, Celniker SE, Reinke V, Waterston RH.
Kudron M, et al.
bioRxiv [Preprint]. 2024 Jan 20:2024.01.18.576242. doi: 10.1101/2024.01.18.576242.
bioRxiv. 2024.
PMID: 38293065
Free PMC article.
Preprint.
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