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Structure-based protein function prediction using graph convolutional networks.
Gligorijević V, Renfrew PD, Kosciolek T, Leman JK, Berenberg D, Vatanen T, Chandler C, Taylor BC, Fisk IM, Vlamakis H, Xavier RJ, Knight R, Cho K, Bonneau R. Gligorijević V, et al. Among authors: berenberg d. Nat Commun. 2021 May 26;12(1):3168. doi: 10.1038/s41467-021-23303-9. Nat Commun. 2021. PMID: 34039967 Free PMC article.
Sequence-structure-function relationships in the microbial protein universe.
Koehler Leman J, Szczerbiak P, Renfrew PD, Gligorijevic V, Berenberg D, Vatanen T, Taylor BC, Chandler C, Janssen S, Pataki A, Carriero N, Fisk I, Xavier RJ, Knight R, Bonneau R, Kosciolek T. Koehler Leman J, et al. Among authors: berenberg d. Nat Commun. 2023 Apr 26;14(1):2351. doi: 10.1038/s41467-023-37896-w. Nat Commun. 2023. PMID: 37100781 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. Among authors: berenberg d. ArXiv [Preprint]. 2023 Aug 10:arXiv:2308.05326v1. ArXiv. 2023. PMID: 37608940 Free PMC article. Preprint.
Protein remote homology detection and structural alignment using deep learning.
Hamamsy T, Morton JT, Blackwell R, Berenberg D, Carriero N, Gligorijevic V, Strauss CEM, Leman JK, Cho K, Bonneau R. Hamamsy T, et al. Among authors: berenberg d. Nat Biotechnol. 2023 Sep 7. doi: 10.1038/s41587-023-01917-2. Online ahead of print. Nat Biotechnol. 2023. PMID: 37679542
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: berenberg d. Nat Methods. 2024 May 14. doi: 10.1038/s41592-024-02272-z. Online ahead of print. Nat Methods. 2024. PMID: 38744917