How we roll

Publications

Selected PublicationsAll Publications
bioRxiv
Apr
7
//
2025

Predicting specificity of TCR-pMHC interactions using machine learning and biophysical models

Martin Culka, Nicolas W Lounsbury, William Thrift, Santrupti Nerli, Andrew Wallace, Gergo Nikolenyi, Darya Orlova, Kiran Mukhyala, Mohammed AlQuraishi
Yes
bioRxiv
Feb
21
//
2025

AlphaFold as a Prior: Experimental Structure Determination Conditioned on a Pretrained Neural Network

Alisia Fadini, Minhuan Li, Airlie J McCoy, Thomas C Terwilliger, Randy J Read, Doeke Hekstra, Mohammed AlQuraishi
Yes
ICML
Feb
8
//
2025

From Mechanistic Interpretability to Mechanistic Biology: Training, Evaluating, and Interpreting Sparse Autoencoders on Protein Language Models

Etowah Adams, Liam Bai, Minji Lee, Yiyang Yu, Mohammed AlQuraishi
Yes
NeurIPS Time Series in the Age of Large Models Workshop
Dec
15
//
2024

Benchmarking Out-of-the-Box Forecasters of Varying Scales in Biology

Anthony Culos · Mohammed AlQuraishi
Yes
Cell
Dec
12
//
2024

How to Build the Virtual Cell with Artificial Intelligence: Priorities and Opportunities

Charlotte Bunne, Yusuf 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, Nicholas J Sofroniew, Fabian 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
No
PMLR
Nov
16
//
2024

QuickBind: A Light-Weight And Interpretable Molecular Docking Model

Wojtek Treyde, Seohyun Chris Kim, Nazim Bouatta, Mohammed AlQuraishi
Yes
arXiv
May
24
//
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
Yes
Nature Biotechnology
May
23
//
2024

Mapping Variant Effects on Anti-Tumor Hallmarks of Primary Human T Cells with Base-Editing Screens

Zachary Walsh, Parin Shah, Neeharika Kothapalli, Shivem Shah, Gergo Nikolenyi, D. Zack Brodtman, Giuseppe Leuzzi, Meri Rogava, Michael Mu, Patricia Ho, Sinan Abuzaid, Neil Vasan, Mohammed AlQuraishi, Joshua D. Milner, Alberto Ciccia, Johannes Melms, Benjamin Izar
No
Nature Methods
May
14
//
2024

OpenFold: Retraining AF2 Yields New Insights Into Its Learning Mechanisms and Generalization Capacity

G Ahdritz, N Bouatta, C Floristean, S Kadyan, Q Xia, W Gerecke, T O’Donnell, D Berenberg, I Fisk, N Zanichelli, B Zhang, A Nowaczynski, B Wang, M Dziubinska, S Zhang, A Ojewole, M Guney, S Biderman, A Watkins, S Ra, P Lorenzo, L Nivon, B Weitzner, Y Ban, S Chen, M Zhang, C Li, S Song, Y He, P Sorger, E Mostaque, Z Zhang, R Bonneau, M AlQuraishi

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            Research Highlight: Iris Marchal, OpenFold provides insights into AlphaFold2’s learning behavior, Nature Biotechnology 2024

Yes
PEDS
Dec
15
//
2023

Growing Ecosystem of Deep Learning Methods for Modeling Protein-Protein Interactions

Julia Rogers, Gergő Nikolényi, Mohammed AlQuraishi
Yes
Journal of Chemical Information and Modeling
Aug
18
//
2023

A Hybrid Structure-Based Machine Learning Approach for Predicting Kinase Inhibition by Small Molecules

Changchang Liu, Peter Kutchukian, Nhan Nguyen, Mohammed AlQuraishi, Peter Sorger
No
NeurIPS
Aug
10
//
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
No
Genome Biology
May
10
//
2023

High-throughput Deep Learning Variant Effect Prediction with Sequence UNET

Alistair S. Dunham, Pedro Beltrao, Mohammed AlQuraishi
Yes
Nature Structural & Molecular Biology
Feb
16
//
2023

Structural Biology at the Scale of Proteomes

Nazim Bouatta, Mohammed AlQuraishi
ICML
Jan
29
//
2023

Generating Novel, Designable, and Diverse Protein Structures by Equivariantly Diffusing Oriented Residue Clouds

Yeqing Lin, Mohammed AlQuraishi
Yes
arXiv
Nov
20
//
2022

Computational Structure Prediction Methods Enable the Systematic Identification of Oncogenic Mutations

Xi Fu, Clara Reglero, Vinay Swamy, Jui Wan Loh, Hossein Khiabanian, Robert Albero, Farhad Forouhar, Mohammed AlQuraishi, Adolfo A. Ferrando, Raul Rabadan
No
Nature Biotechnology
Oct
3
//
2022

Single-Sequence Protein Structure Prediction Using a Language Model and Deep Learning

Ratul Chowdhury, Nazim Bouatta, Surojit Biswas, Christina Floristean, Anant Kharkar, Koushik Roy, Charlotte Rochereau, Gustaf Ahdritz, Joanna Zhang, George M. Church, Peter K. Sorger, Mohammed AlQuraishi
Yes
bioRxiv
Oct
2
//
2022

Predicting Enzyme Substrate Chemical Structure with Protein Language Models

Adrian Jinich, Sakila Z. Nazia, Andrea V. Tellez, Dmitrij Rappoport, Mohammed AlQuraishi, Kyu Rhee
No
Cell
Jul
21
//
2022

The Next Decade of Protein Structure

Corinne A. Lutomski, Tarick J. El-Baba, Carol V. Robinson, Roland Riek, Sjors H.W. Scheres, Nieng Yan, Mohammed AlQuraishi, Lu Gan
No
Current Opinion in Chemical Biology
Dec
1
//
2021

Machine Learning in Protein Structure Prediction

Mohammed AlQuraishi
No
Nature Methods
Oct
4
//
2021

Differentiable Biology: Using Deep Learning for Biophysics-based and Data-Driven Modeling of Molecular Mechanisms

Mohammed AlQuraishi, Peter K Sorger
Yes
bioRxiv
Sep
4
//
2021

Protein Structure Prediction Using a Maximum Likelihood Formulation of a Recurrent Geometric Network

Guowei Qi, Mallory R Tollefson, Rose A Gogal, Richard J.H. Smith, Mohammed AlQuraishi, Michael J Schnieders
Nature
Aug
23
//
2021

Protein Structure Prediction Revolutionized

Mohammed AlQuraishi
No
Genome Medicine
Aug
6
//
2021

Recombination and Lineage-specific Mutations Linked to the Emergence of SARS-CoV-2

Juan Ángel Patiño-Galindo, Ioan Filip, Ratul Chowdhury, Costas D. Maranas, Peter K. Sorger, Mohammed AlQuraishi, Raul Rabadan
No
Acta Crystallographica D
Jul
29
//
2021

Protein Structure Prediction by AlphaFold2: Are Attention and Symmetries All You Need?

Nazim Bouatta, Peter Sorger, Mohammed AlQuraishi
Nature
Jan
15
//
2020

A Watershed Moment for Protein Structure Prediction

Mohammed AlQuraishi
No
Nature Methods
Jan
6
//
2020

Biophysical Prediction of Protein–Peptide Interactions and Signaling Networks Using Machine Learning

Joseph M Cunningham, Grigoriy Koytiger, Peter K Sorger, Mohammed AlQuraishi
Yes
Bioinformatics
Nov
15
//
2019

AlphaFold at CASP13

Mohammed AlQuraishi
No
arXiv
Nov
9
//
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, Sashank Karri, Anand Kannan, Antonio Moretti, Mohammed AlQuraishi, Chen Keasar, Itsik Pe'er
No
Nature Methods
Oct
21
//
2019

Unified Rational Protein Engineering with Sequence-Based Deep Representation Learning

Ethan C Alley, Grigory Khimulya, Surojit Biswas, Mohammed AlQuraishi, George M Church
Yes
BMC Bioinformatics
Jun
11
//
2019

ProteinNet: A Standardized Data Set for Machine Learning of Protein Structure

Mohammed AlQuraishi
No
Cell Systems
Apr
24
//
2019

End-to-End Differentiable Learning of Protein Structure

Mohammed AlQuraishi
Yes
Journal of Computational Chemistry
Jan
7
//
2019

pNeRF: Parallelized Conversion from Internal to Cartesian Coordinates

Mohammed AlQuraishi
No
Science Translational Medicine
May
18
//
2016

Reproducibility Will Only Come with Data Liberation

Mohammed AlQuraishi, Peter K Sorger
No
BMC Bioinformatics
Nov
19
//
2015

An Affinity-Structure Database of Helix-Turn-Helix:DNA Complexes with a Universal Coordinate System

Mohammed AlQuraishi, Shengdong Tang, Xide Xia
No
Nature Genetics
Nov
2
//
2014

A Multiscale Statistical Mechanical Framework Integrates Biophysical and Genomic Data to Assemble Cancer Networks

Mohammed AlQuraishi, Grigoriy Koytiger, Anne Jenney, Gavin MacBeath, Peter K Sorger

Yes
Proteins
Oct
8
//
2012

Three Enhancements to The Inference of Statistical Protein‐DNA Potentials

Mohammed AlQuraishi, Harley H McAdams
No
PNAS
Sep
6
//
2011

Direct Inference of Protein–DNA Interactions Using Compressed Sensing Methods

Mohammed AlQuraishi, Harley H McAdams
Yes