AlQuraishi, Mohammed

Unified rational protein engineering with sequence-based deep representation learning

Alley, E. C., Khimulya, G., Biswas, S., AlQuraishi, M., & Church, G. M. (2019) · Nature Methods

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 1,131

Single-sequence protein structure prediction using language models from deep learning

Chowdhury, R., Bouatta, N., Biswas, S., Rochereau, C., Church, G. M., Sorger, P. K., & AlQuraishi, M. (2021) · Nature Biotechnology

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 455

Single-sequence protein structure prediction using a language model and deep learning

Chowdhury, R., Bouatta, N., Biswas, S., Floristean, C., Kharkar, A., Roy, K., Rochereau, C., Ahdritz, G., Zhang, J., Church, G. M., et al. (2022) · Nature Biotechnology

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 455

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, T. J., Berenberg, D., Fisk, I., Zanichelli, N., et al. (2024) · Nature Methods

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 439

End-to-End Differentiable Learning of Protein Structure

AlQuraishi, M. (2019) · Cell Systems

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 371

Biophysical prediction of protein–peptide interactions and signaling networks using machine learning

Cunningham, J. M., Rogers, J. R., Koytiger, G., Sorger, P. K., & AlQuraishi, M. (2020) · Nature Methods

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 108

Differentiable biology: using deep learning for biophysics-based and data-driven modeling of molecular mechanisms

AlQuraishi, M., & Sorger, P. K. (2021) · Nature Methods

Machine Learning in BioinformaticsGene Regulatory Network Analysis

Cited by 96

Protein structure prediction by AlphaFold 2: are attention and symmetries all you need?

Bouatta, N., Sorger, P., & AlQuraishi, M. (2021) · Acta Crystallographica Section D Structural Biology

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 69

High-throughput deep learning variant effect prediction with Sequence UNET

Dunham, A. S., Beltrao, P., & AlQuraishi, M. (2023) · Genome Biology

Genomics and Rare DiseasesMachine Learning in Bioinformatics

Cited by 31

AlphaFold as a prior: experimental structure determination conditioned on a pretrained neural network

Fadini, A., Li, M., McCoy, A. J., Banjara, S., Okumura, H., Napier, E., Fontana, P., Khan, A. R., Jovine, L., Terwilliger, T. C., et al. (2026) · Nature Methods

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 22