Mohammed AlQuraishi

18 papers A* 3Journal 14Unranked 1

Year	Rank	Type	Title / Venue / Authors
2025	A*	`conf`	From Mechanistic Interpretability to Mechanistic Biology: Training, Evaluating, and Interpreting Sparse Autoencoders on Protein Language Models. ICML Etowah Adams, Liam Bai, Minji Lee, Yiyang Yu, Mohammed AlQuraishi
2024	J	`jnl`	How to Build the Virtual Cell with Artificial Intelligence: Priorities and Opportunities. CoRR Charlotte Bunne, Yusuf H. Roohani, Yanay Rosen, Ankit Gupta, Xikun Zhang, Marcel Roed, Theo Alexandrov, Mohammed AlQuraishi, Patricia Brennan, Daniel B. Burkhardt, Andrea Califano, Jonah Cool, Abby F. Dernburg, Kirsty Ewing, Emily B. Fox, Matthias Haury, Amy E. Herr, Eric Horvitz, Patrick D. Hsu, Viren Jain, Gregory R. Johnson, Thomas Kalil, David R. Kelley, Shana O. Kelley, Anna Kreshuk, Tim Mitchison, Stephani Otte, Jay Shendure, Nicolas J. Sofroniew, Fabian J. Theis, Christina V. Theodoris, Srigokul Upadhyayula, Marc Valer, Bo Wang, Eric Xing, Serena Yeung-Levy, Marinka Zitnik, Theofanis Karaletsos, Aviv Regev, Emma Lundberg, Jure Leskovec, Stephen R. Quake
2024	J	`jnl`	Out of Many, One: Designing and Scaffolding Proteins at the Scale of the Structural Universe with Genie 2. CoRR Yeqing Lin, Minji Lee, Zhao Zhang, Mohammed AlQuraishi
2024	—	`conf`	QuickBind: A Light-Weight And Interpretable Molecular Docking Model. MLCB Wojtek Treyde, Seohyun Chris Kim, Nazim Bouatta, Mohammed AlQuraishi
2024	J	`jnl`	QuickBind: A Light-Weight And Interpretable Molecular Docking Model. CoRR Wojtek Treyde, Seohyun Chris Kim, Nazim Bouatta, Mohammed AlQuraishi
2023	J	`jnl`	A Hybrid Structure-Based Machine Learning Approach for Predicting Kinase Inhibition by Small Molecules. J. Chem. Inf. Model. Changchang Liu, Peter Kutchukian, Nhan D. Nguyen, Mohammed AlQuraishi, Peter K. Sorger
2023	J	`jnl`	DeepSpeed4Science Initiative: Enabling Large-Scale Scientific Discovery through Sophisticated AI System Technologies. CoRR Shuaiwen Leon Song, Bonnie Kruft, Minjia Zhang, Conglong Li, Shiyang Chen, Chengming Zhang, Masahiro Tanaka, Xiaoxia Wu, Jeff Rasley, Ammar Ahmad Awan, Connor Holmes, Martin Cai, Adam Ghanem, Zhongzhu Zhou, Yuxiong He, Pete Luferenko, Divya Kumar, Jonathan A. Weyn, Ruixiong Zhang, Sylwester Klocek, Volodymyr Vragov, Mohammed AlQuraishi, Gustaf Ahdritz, Christina Floristean, Cristina Negri, Rao Kotamarthi, Venkatram Vishwanath, Arvind Ramanathan, Sam Foreman, Kyle Hippe, Troy Arcomano, Romit Maulik, Maxim Zvyagin, Alexander Brace, Bin Zhang, Cindy Orozco Bohorquez, Austin Clyde, Bharat Kale, Danilo Perez-Rivera, Heng Ma, Carla M. Mann, Michael W. Irvin, J. Gregory Pauloski, Logan T. Ward, Valérie Hayot-Sasson, Murali Emani, Zhen Xie, Diangen Lin, Maulik Shukla, Ian T. Foster, James J. Davis, Michael E. Papka, Thomas S. Brettin, Prasanna Balaprakash, Gina Tourassi, John Gounley, Heidi A. Hanson, Thomas E. Potok, Massimiliano Lupo Pasini, Kate Evans, Dan Lu, Dalton D. Lunga, Junqi Yin, Sajal Dash, Feiyi Wang, Mallikarjun Shankar, Isaac Lyngaas, Xiao Wang, Guojing Cong, Pei Zhang, Ming Fan, Siyan Liu, Adolfy Hoisie, Shinjae Yoo, Yihui Ren, William Tang, Kyle Felker, Alexey Svyatkovskiy, Hang Liu, Ashwin M. Aji, Angela Dalton, Michael J. Schulte, Karl W. Schulz, Yuntian Deng, Weili Nie, Josh Romero, Christian Dallago, Arash Vahdat, Chaowei Xiao, Thomas Gibbs, Anima Anandkumar, Rick Stevens
2023	A*	`conf`	Generating Novel, Designable, and Diverse Protein Structures by Equivariantly Diffusing Oriented Residue Clouds. ICML Yeqing Lin, Mohammed AlQuraishi
2023	J	`jnl`	Generating Novel, Designable, and Diverse Protein Structures by Equivariantly Diffusing Oriented Residue Clouds. CoRR Yeqing Lin, Mohammed AlQuraishi
2023	J	`jnl`	Growing ecosystem of deep learning methods for modeling protein-protein interactions. CoRR Julia R. Rogers, Gergo Nikolényi, Mohammed AlQuraishi
2023	A*	`conf`	OpenProteinSet: Training data for structural biology at scale. NeurIPS Gustaf Ahdritz, Nazim Bouatta, Sachin Kadyan, Lukas Jarosch, Daniel Berenberg, Ian Fisk, Andrew M. Watkins, Stephen Ra, Richard Bonneau, Mohammed AlQuraishi
2023	J	`jnl`	OpenProteinSet: Training data for structural biology at scale. CoRR Gustaf Ahdritz, Nazim Bouatta, Sachin Kadyan, Lukas Jarosch, Daniel Berenberg, Ian Fisk, Andrew M. Watkins, Stephen Ra, Richard Bonneau, Mohammed AlQuraishi
2019	J	`jnl`	Accurate Protein Structure Prediction by Embeddings and Deep Learning Representations. CoRR Iddo Drori, Darshan Thaker, Arjun Srivatsa, Daniel Jeong, Yueqi Wang, Linyong Nan, Fan Wu, Dimitri Leggas, Jinhao Lei, Weiyi Lu, Weilong Fu, Yuan Gao, Sashank Karri, Anand Kannan, Antonio Khalil Moretti, Mohammed AlQuraishi, Chen Keasar, Itsik Pe'er
2019	J	`jnl`	AlphaFold at CASP13. Bioinform. Mohammed AlQuraishi
2019	J	`jnl`	Parallelized Natural Extension Reference Frame: Parallelized Conversion from Internal to Cartesian Coordinates. J. Comput. Chem. Mohammed AlQuraishi
2019	J	`jnl`	ProteinNet: a standardized data set for machine learning of protein structure. BMC Bioinform. Mohammed AlQuraishi
2019	J	`jnl`	ProteinNet: a standardized data set for machine learning of protein structure. CoRR Mohammed AlQuraishi
2015	J	`jnl`	An affinity-structure database of helix-turn-helix: DNA complexes with a universal coordinate system. BMC Bioinform. Mohammed AlQuraishi, Shengdong Tang, Xide Xia