Author

Nathaniel Corley

University of WashingtonORCID 0000-0002-6509-7144Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Approach:deep learning· 3 Research Focus:protein design· 3 Assay:protein sequence· 3 Approach:diffusion model· 2 Approach:experimental assay· 2 Assay:protein structure· 2 Research Focus:protein structure prediction· 2 Research Focus:software / tool· 2

Frequent Co-Authors

David A. BakeriD· 3 shared Bo QiangiD· 2 shared Frank DiMaioiD· 2 shared Jasper ButcheriD· 2 shared Jonathan FunkiD· 2 shared Kieran DidiiD· 2 shared Magnus S. BaueriD· 2 shared Maxwell W. KazmaniD· 2 shared

Activity by Year

2025-2026 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

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3 shared papersBiochemistry

David A. BakerORCID

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Author profile →

4 papers

Recent·Most cited

Design of readers for pathological PTM proteoforms in Alzheimer's disease

Kejia Wu, Tiana Schantz, Lemuel Chang, Prarthna Chabria, Elaina Bashaw, Thejesh Reddy Kalatturu, Doo Yeon Kim, An‐Qi Chen, Nathaniel Corley, Asim K. Bera, Alex Kang, Hannah Nguyen, Johnny Mendoza, Xinting Li, Magnus S. Bauer, , David A. Baker

The paper designs and validates protein readers that specifically detect disease-related modifications in Tau and Abeta in Alzheimer's disease models and human samples.

bioRxiv · Oct 21, 2026 · PreprintBioengineering

De novo Design of All-atom Biomolecular Interactions with RFdiffusion3

Jasper Butcher, Rohith Krishna, Raktim Mitra, Rafael I. Brent, Yanjing Li, Nathaniel Corley, Paul T. Kim, Jonathan Funk, Simon V. Mathis, Saman Salike, Aiko Muraishi, Helen E. Eisenach, Tuscan Rock Thompson, Jie Chen, Yuliya Politanska, , David A. Baker

An all-atom diffusion model using a 14-atom residue representation and sparse U-Net architecture accelerates biomolecular design 10-fold, enabling experimentally validated DNA-binding proteins and multi-turnover cysteine hydrolases.

bioRxiv · Sep 18, 2025 · PreprintBiochemistry✦ In-depth digest

Accelerating Biomolecular Modeling with AtomWorks andRF3

Nathaniel Corley, Simon V. Mathis, Rohith Krishna, Magnus S. Bauer, Tuscan R. Thompson, Woody Ahern, Maxwell W. Kazman, Rafael I. Brent, Kieran Didi, Andrew Kubaney, Ryan McHugh, Arnav Nagle, Andrew Favor, Meghana Kshirsagar, Pascal Sturmfels, , Frank DiMaio

AtomWorks, a modular atom-level data framework, trains structure prediction and design models; the resulting RF3 improves chirality handling and performs between AF3 and Boltz.

bioRxiv · Aug 14, 2025 · PreprintBiochemistry✦ In-depth digest

ProtNote: a multimodal method for protein-function annotation

Samir Char, Nathaniel Corley, Sarah Alamdari, Kevin Yang, Ava P. Amini

ProtNote is a multimodal deep learning model that enables supervised and zero-shot protein function prediction using free-form text inputs, generalizing to unseen functions.

Bioinformatics · Apr 12, 2025Peer-reviewedBioengineering