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Structure-based protein function prediction using graph convolutional networks.
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.
Nat Commun. 2023 Apr 26;14(1):2351. doi: 10.1038/s41467-023-37896-w.
Nat Commun. 2023.
PMID: 37100781
Free PMC article.
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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.
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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.
Nat Methods. 2024 May 14. doi: 10.1038/s41592-024-02272-z. Online ahead of print.
Nat Methods. 2024.
PMID: 38744917
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GIANT API: an application programming interface for functional genomics.
Roberts AM, Wong AK, Fisk I, Troyanskaya OG.
Roberts AM, et al.
Nucleic Acids Res. 2016 Jul 8;44(W1):W587-92. doi: 10.1093/nar/gkw289. Epub 2016 Apr 20.
Nucleic Acids Res. 2016.
PMID: 27098035
Free PMC article.
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