Author

J. E. Stone

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Biophysics· 3

Signature Assays, Organisms & Methods

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Approach:deep learning· 3 Approach:simulation· 2 Research Focus:cell signaling & trafficking· 1 Assay:cryo-EM· 1 Organism:human· 1 Assay:multiome· 1 Research Focus:protein folding & dynamics· 1 Research Focus:protein structure prediction· 1

Frequent Co-Authors

A. Brace· 2 shared A. Ramanathan· 2 shared A. Trifan· 2 shared D. Hardy· 2 shared H. Ma· 2 shared J. Phillips· 2 shared L. Huang· 2 shared T. Gibbs· 2 shared

Activity by Year

2019-2021 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 44 mutual co-author links

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2 shared papersBiophysics

A. Brace

Mutual co-authors in cluster

Author profile →

3 papers

Recent·Most cited

Intelligent Resolution: Integrating Cryo-EM with AI-driven Multi-resolution Simulations to Observe the SARS-CoV-2 Replication-Transcription Machinery in Action

A. Trifan, D. Gorgun, Z. Li, A. Brace, M. Zvyagin, H. Ma, A. R. Clyde, D. A. Clark, M. Salim, D. Hardy, T. Burnley, L. Huang, J. McCalpin, M. Emani, H. Yoo, , A. Ramanathan

This study develops an AI-driven multi-resolution simulation workflow to study SARS-CoV-2 RTC dynamics, combining cryo-EM with mesoscale simulations and AI methods.

bioRxiv · Oct 9, 2021 · PreprintBiophysics

AI-Driven Multiscale Simulations Illuminate Mechanisms of SARS-CoV-2 Spike Dynamics

L. Casalino, A. C. Dommer, Z. Gaieb, E. P. Barros, T. Sztain, S.-H. Ahn, A. Trifan, A. Brace, H. Ma, H. Lee, M. Turilli, A. Bogetti, S. Khalid, L. Chong, C. Simmerling, , R. E. Amaro

This paper develops an AI-driven workflow to simulate SARS-CoV-2 spike protein dynamics, revealing glycan shield structure, spike glycans' role in infectivity, and spike-ACE2 interactions.

bioRxiv · Nov 19, 2020Biophysics

High-performance analysis of biomolecular containers to measure small-molecule transport, transbilayer lipid diffusion, and protein cavities

A. J. Bryer, J. A. Hadden, J. E. Stone, J. R. Perilla

The paper introduces a 3D ray casting method to classify space inside and outside biomolecular containers, enabling efficient analysis of small-molecule transport, lipid diffusion, and protein cavities in molecular dynamics simulations.

bioRxiv · Jul 13, 2019Biophysics