Recent Publications

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

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

Protein structure prediction by AlphaFold2: are attention and symmetries all you need?
Bouatta N,  
Sorger P,  AlQuraishi M. (2021)
Acta Crystallographica D