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RNA3DB: A structurally-dissimilar dataset split for training and benchmarking deep learning models for RNA structure prediction.
Szikszai M, Magnus M, Sanghi S, Kadyan S, Bouatta N, Rivas E. Szikszai M, et al. Among authors: kadyan s. bioRxiv [Preprint]. 2024 Mar 11:2024.01.30.578025. doi: 10.1101/2024.01.30.578025. bioRxiv. 2024. Update in: J Mol Biol. 2024 Sep 1;436(17):168552. doi: 10.1016/j.jmb.2024.168552 PMID: 38352531 Free PMC article. Updated. 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: kadyan s. 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. Among authors: kadyan s. Nat Methods. 2024 Aug;21(8):1514-1524. doi: 10.1038/s41592-024-02272-z. Epub 2024 May 14. Nat Methods. 2024. PMID: 38744917
31 results