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Page 1
De novo designed proteins neutralize lethal snake venom toxins.
Vázquez Torres S, Benard Valle M, Mackessy SP, Menzies SK, Casewell NR, Ahmadi S, Burlet NJ, Muratspahić E, Sappington I, Overath MD, Rivera-de-Torre E, Ledergerber J, Laustsen AH, Boddum K, Bera AK, Kang A, Brackenbrough E, Cardoso IA, Crittenden EP, Edge RJ, Decarreau J, Ragotte RJ, Pillai AS, Abedi M, Han HL, Gerben SR, Murray A, Skotheim R, Stuart L, Stewart L, Fryer TJA, Jenkins TP, Baker D. Vázquez Torres S, et al. Among authors: brackenbrough e. Nature. 2025 Jan 15. doi: 10.1038/s41586-024-08393-x. Online ahead of print. Nature. 2025. PMID: 39814879
Accurate de novo design of high-affinity protein binding macrocycles using deep learning.
Rettie SA, Juergens D, Adebomi V, Bueso YF, Zhao Q, Leveille AN, Liu A, Bera AK, Wilms JA, Üffing A, Kang A, Brackenbrough E, Lamb M, Gerben SR, Murray A, Levine PM, Schneider M, Vasireddy V, Ovchinnikov S, Weiergräber OH, Willbold D, Kritzer JA, Mougous JD, Baker D, DiMaio F, Bhardwaj G. Rettie SA, et al. Among authors: brackenbrough e. bioRxiv [Preprint]. 2024 Nov 18:2024.11.18.622547. doi: 10.1101/2024.11.18.622547. bioRxiv. 2024. PMID: 39605685 Free PMC article. Preprint.
Design of facilitated dissociation enables control over cytokine signaling duration.
Broerman AJ, Pollmann C, Lichtenstein MA, Jackson MD, Tessmer MH, Ryu WH, Abedi MH, Sahtoe DD, Allen A, Kang A, De La Cruz J, Brackenbrough E, Sankaran B, Bera AK, Zuckerman DM, Stoll S, Praetorius F, Piehler J, Baker D. Broerman AJ, et al. Among authors: brackenbrough e. bioRxiv [Preprint]. 2024 Nov 16:2024.11.15.623900. doi: 10.1101/2024.11.15.623900. bioRxiv. 2024. PMID: 39605600 Free PMC article. Preprint.
Publisher Correction: Multistate and functional protein design using RoseTTAFold sequence space diffusion.
Lisanza SL, Gershon JM, Tipps SWK, Sims JN, Arnoldt L, Hendel SJ, Simma MK, Liu G, Yase M, Wu H, Tharp CD, Li X, Kang A, Brackenbrough E, Bera AK, Gerben S, Wittmann BJ, McShan AC, Baker D. Lisanza SL, et al. Among authors: brackenbrough e. Nat Biotechnol. 2024 Oct 7. doi: 10.1038/s41587-024-02456-0. Online ahead of print. Nat Biotechnol. 2024. PMID: 39375454 No abstract available.
Multistate and functional protein design using RoseTTAFold sequence space diffusion.
Lisanza SL, Gershon JM, Tipps SWK, Sims JN, Arnoldt L, Hendel SJ, Simma MK, Liu G, Yase M, Wu H, Tharp CD, Li X, Kang A, Brackenbrough E, Bera AK, Gerben S, Wittmann BJ, McShan AC, Baker D. Lisanza SL, et al. Among authors: brackenbrough e. Nat Biotechnol. 2024 Sep 25. doi: 10.1038/s41587-024-02395-w. Online ahead of print. Nat Biotechnol. 2024. PMID: 39322764
Computational design of serine hydrolases.
Lauko A, Pellock SJ, Anischanka I, Sumida KH, Juergens D, Ahern W, Shida A, Hunt A, Kalvet I, Norn C, Humphreys IR, Jamieson C, Kang A, Brackenbrough E, Bera AK, Sankaran B, Houk KN, Baker D. Lauko A, et al. Among authors: brackenbrough e. bioRxiv [Preprint]. 2024 Aug 30:2024.08.29.610411. doi: 10.1101/2024.08.29.610411. bioRxiv. 2024. PMID: 39257749 Free PMC article. Preprint.
Diffusing protein binders to intrinsically disordered proteins.
Liu C, Wu K, Choi H, Han H, Zhang X, Watson JL, Shijo S, Bera AK, Kang A, Brackenbrough E, Coventry B, Hick DR, Hoofnagle AN, Zhu P, Li X, Decarreau J, Gerben SR, Yang W, Wang X, Lamp M, Murray A, Bauer M, Baker D. Liu C, et al. Among authors: brackenbrough e. bioRxiv [Preprint]. 2024 Jul 16:2024.07.16.603789. doi: 10.1101/2024.07.16.603789. bioRxiv. 2024. PMID: 39071267 Free PMC article. Preprint.
De novo designed proteins neutralize lethal snake venom toxins.
Torres SV, Valle MB, Mackessy SP, Menzies SK, Casewell NR, Ahmadi S, Burlet NJ, Muratspahić E, Sappington I, Overath MD, Rivera-de-Torre E, Ledergerber J, Laustsen AH, Boddum K, Bera AK, Kang A, Brackenbrough E, Cardoso IA, Crittenden EP, Edge RJ, Decarreau J, Ragotte RJ, Pillai AS, Abedi M, Han HL, Gerben SR, Murray A, Skotheim R, Stuart L, Stewart L, Fryer TJA, Jenkins TP, Baker D. Torres SV, et al. Among authors: brackenbrough e. Res Sq [Preprint]. 2024 May 17:rs.3.rs-4402792. doi: 10.21203/rs.3.rs-4402792/v1. Res Sq. 2024. Update in: Nature. 2025 Jan 15. doi: 10.1038/s41586-024-08393-x PMID: 38798548 Free PMC article. Updated. Preprint.
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. Among authors: brackenbrough e. Science. 2024 Apr 19;384(6693):eadl2528. doi: 10.1126/science.adl2528. Epub 2024 Apr 19. Science. 2024. PMID: 38452047 Free article.