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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: watkins am. Nat Methods. 2024 Aug;21(8):1514-1524. doi: 10.1038/s41592-024-02272-z. Epub 2024 May 14. Nat Methods. 2024. PMID: 38744917
Local structural flexibility drives oligomorphism in computationally designed protein assemblies.
Khmelinskaia A, Bethel NP, Fatehi F, Antanasijevic A, Borst AJ, Lai SH, Wang JYJ, Mallik BB, Miranda MC, Watkins AM, Ogohara C, Caldwell S, Wu M, Heck AJR, Veesler D, Ward AB, Baker D, Twarock R, King NP. Khmelinskaia A, et al. Among authors: watkins am. bioRxiv [Preprint]. 2023 Oct 19:2023.10.18.562842. doi: 10.1101/2023.10.18.562842. bioRxiv. 2023. PMID: 37905007 Free PMC article. Preprint.
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. Among authors: watkins am. ArXiv [Preprint]. 2023 Aug 10:arXiv:2308.05326v1. ArXiv. 2023. PMID: 37608940 Free PMC article. Preprint.
Macrocyclic β-Sheets Stabilized by Hydrogen Bond Surrogates.
Nazzaro A, Lu B, Sawyer N, Watkins AM, Arora PS. Nazzaro A, et al. Among authors: watkins am. Angew Chem Int Ed Engl. 2023 Oct 9;62(41):e202303943. doi: 10.1002/anie.202303943. Epub 2023 Jun 2. Angew Chem Int Ed Engl. 2023. PMID: 37170337 Free PMC article.
65 results