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Single-sequence protein structure prediction using a language model and deep learning.
Chowdhury R, Bouatta N, Biswas S, Floristean C, Kharkar A, Roy K, Rochereau C, Ahdritz G, Zhang J, Church GM, Sorger PK, AlQuraishi M. Chowdhury R, et al. Among authors: ahdritz g. Nat Biotechnol. 2022 Nov;40(11):1617-1623. doi: 10.1038/s41587-022-01432-w. Epub 2022 Oct 3. Nat Biotechnol. 2022. PMID: 36192636 Free PMC article.
OpenProteinSet: Training data for structural biology at scale.
Ahdritz G, Bouatta N, Kadyan S, Jarosch L, Berenberg D, Fisk I, Watkins AM, Ra S, Bonneau R, AlQuraishi M. Ahdritz G, et al. ArXiv [Preprint]. 2023 Aug 10:arXiv:2308.05326v1. ArXiv. 2023. PMID: 37608940 Free PMC article. Preprint.
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. Nat Methods. 2024 May 14. doi: 10.1038/s41592-024-02272-z. Online ahead of print. Nat Methods. 2024. PMID: 38744917