An affinity-structure database of helix-turn-helix: DNA complexes with a universal coordinate system. - Mohammed AlQuraishi; Shengdong Tang; Xide Xia (BMC Bioinform., 2015)

AlphaFold at CASP13. - Mohammed AlQuraishi (Bioinform., 2019)

ProteinNet: a standardized data set for machine learning of protein structure. - Mohammed AlQuraishi (BMC Bioinform., 2019)

Accurate Protein Structure Prediction by Embeddings and Deep Learning Representations. - Iddo Drori; Darshan Thaker; Arjun Srivatsa; Daniel Jeong; Yueqi Wang; Linyong Nan; Fan Wu; Dimitri Leggas; Jinhao Lei; Weiyi Lu; Weilong Fu; Yuan Gao; et al. (CoRR, 2019)

Parallelized Natural Extension Reference Frame: Parallelized Conversion from Internal to Cartesian Coordinates. - Mohammed AlQuraishi (J. Comput. Chem., 2019)

Generating Novel, Designable, and Diverse Protein Structures by Equivariantly Diffusing Oriented Residue Clouds. - Yeqing Lin; Mohammed AlQuraishi (ICML, 2023)

OpenProteinSet: Training data for structural biology at scale. - Gustaf Ahdritz; Nazim Bouatta; Sachin Kadyan; Lukas Jarosch; Daniel Berenberg; Ian Fisk; Andrew M. Watkins; Stephen Ra; Richard Bonneau; Mohammed AlQuraishi (NeurIPS, 2023)

DeepSpeed4Science Initiative: Enabling Large-Scale Scientific Discovery through Sophisticated AI System Technologies. - Shuaiwen Leon Song; Bonnie Kruft; Minjia Zhang; Conglong Li; Shiyang Chen 004; Chengming Zhang 006; Masahiro Tanaka; Xiaoxia Wu; Jeff Rasley; Ammar Ahmad Awan; Connor Holmes; Martin Cai; et al. (CoRR, 2023)

Growing ecosystem of deep learning methods for modeling protein-protein interactions. - Julia R. Rogers; Gergo Nikolényi; Mohammed AlQuraishi (CoRR, 2023)

QuickBind: A Light-Weight And Interpretable Molecular Docking Model. - Wojtek Treyde; Seohyun Chris Kim; Nazim Bouatta; Mohammed AlQuraishi (MLCB, 2024)

Out of Many, One: Designing and Scaffolding Proteins at the Scale of the Structural Universe with Genie 2. - Yeqing Lin; Minji Lee; Zhao Zhang; Mohammed AlQuraishi (CoRR, 2024)

How to Build the Virtual Cell with Artificial Intelligence: Priorities and Opportunities. - Charlotte Bunne; Yusuf H. Roohani; Yanay Rosen; Ankit Gupta; Xikun Zhang 001; Marcel Roed; Theo Alexandrov; Mohammed AlQuraishi; Patricia Brennan; Daniel B. Burkhardt; Andrea Califano; Jonah Cool; et al. (CoRR, 2024)