†Corresponding author, #First author
RNA3DB: A dataset for training and benchmarking deep learning models for RNA structure prediction
Szikszai M, Magnus M, Sanghi S, Kadyan S, Bouatta N, Rivas E. (2024)
bioRxiv (submitted)
OpenProteinSet: Training data for structural biology at scale
Ahdritz G, Bouatta N,† Kadyan S, Jarosch L, Berenberg D, Fisk I, Watkins A, Ra S, Bonneau R, AlQuraishi M. (2023)
Accepted in NeurIPS 2023
- The largest database for training AlphaFold2-like systems.
- Featured by Hugging Face Daily Papers.
Structural biology at the scale of proteomes
Bouatta N,† and AlQuraishi M. (2023)
Nature Structural & Molecular Biology
OpenFold: Retraining AlphaFold2 yields new insights into its learning mechanisms and capacity for generalization
Ahdritz G, Bouatta N,†,# Kadyan S, Xia Q, Gerecke W, O'Donnell T, Berenberg D, Fisk I, Zanichelli N, Zhang B, Nowaczynski A, Wang B, Stepniewska-Dziubinska M, Zhang S, Ojewole A, Guney M, Biderman S, Watkins A, Ra S, Lorenzo P, Nivon L, Weitzner B, Ban Y, Sorger P, Mostaque E, Zhang Z, Bonneau R, AlQuraishi M. (2022)
Accepted in Nature Methods
- Media coverage: Didero, TechCrunch, Weights & Biases, GeekWire, Riken.
- OpenFold software is offered as a service by leading cloud and compute providers, including Amazon (I, II) and NVIDIA (I, II).
- Used by Meta AI for the creation of the ESM Metagenomic Atlas, which contains over 600 million predicted protein structures.
Single-sequence protein structure prediction using language models and deep learning
Chowdhury R, Bouatta N,†,# Biswas S, Floristean C, Rochereau C, Kharkar A, Ahdritz G, Zhang J, Church G, Sorger P, and AlQuraishi M. (2022).
Nature Biotechnology
- Featured as the cover of the Nov. 2022 issue of Nature Biotechnology.
- Associated commentary: Michaud J, Madani A, Fraser J. (2022) A language model beats alphafold2 on orphans. Nature Biotechnology.
- Derek Lowe (2021) Another Way to Do Protein Structure Prediction, In the Pipeline, Science.
- More coverage: More coverage: Forbes (I, II)
Protein structure prediction by AlphaFold2: are attention and symmetries all you need?
Bouatta N,† Sorger P, AlQuraishi M. (2021)
Acta Crystallographica D
- Featured as the cover of the August 2021 issue of Acta Crystallographica D.
- Faculty of 1000