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OpenFold: retraining AlphaFold2 yields new insights into its learning mechanisms and capacity for generalization.
Ahdritz G, Bouatta N, Floristean C, Kadyan S, Xia Q, Gerecke W, O'Donnell TJ, Berenberg D, Fisk I, Zanichelli N, Zhang B, Nowaczynski A, Wang B, Stepniewska-Dziubinska MM, Zhang S, Ojewole A, Guney ME, Biderman S, Watkins AM, Ra S, Lorenzo PR, Nivon L, Weitzner B, Ban YA, Chen S, Zhang M, Li C, Song SL, He Y, Sorger PK, Mostaque E, Zhang Z, Bonneau R, AlQuraishi M. Ahdritz G, et al. Among authors: o donnell tj. Nat Methods. 2024 Aug;21(8):1514-1524. doi: 10.1038/s41592-024-02272-z. Epub 2024 May 14. Nat Methods. 2024. PMID: 38744917
Anti-inflammatory Quinoline Alkaloids from the Roots of Waltheria indica.
Liu F, O'Donnell TJ, Park EJ, Kovacs S, Nakamura K, Dave A, Luo Y, Sun R, Wall M, Wongwiwatthananukit S, Silva DK, Williams PG, Pezzuto JM, Chang LC. Liu F, et al. Among authors: o donnell tj. J Nat Prod. 2023 Feb 24;86(2):276-289. doi: 10.1021/acs.jnatprod.2c00861. Epub 2023 Feb 6. J Nat Prod. 2023. PMID: 36746775
On TCR binding predictors failing to generalize to unseen peptides.
Grazioli F, Mösch A, Machart P, Li K, Alqassem I, O'Donnell TJ, Min MR. Grazioli F, et al. Among authors: o donnell tj. Front Immunol. 2022 Oct 21;13:1014256. doi: 10.3389/fimmu.2022.1014256. eCollection 2022. Front Immunol. 2022. PMID: 36341448 Free PMC article.
Zinc limitation triggers anticipatory adaptations in Mycobacterium tuberculosis.
Dow A, Sule P, O'Donnell TJ, Burger A, Mattila JT, Antonio B, Vergara K, Marcantonio E, Adams LG, James N, Williams PG, Cirillo JD, Prisic S. Dow A, et al. Among authors: o donnell tj. PLoS Pathog. 2021 May 14;17(5):e1009570. doi: 10.1371/journal.ppat.1009570. eCollection 2021 May. PLoS Pathog. 2021. PMID: 33989345 Free PMC article.
54 results