Author

C. Simmerling

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· 2 Research Focus:benchmarking· 1 Research Focus:clustering· 1 Approach:experimental assay· 1 Research Focus:protein folding & dynamics· 1 Assay:protein structure· 1 Research Focus:protein structure prediction· 1 Approach:simulation· 1

Frequent Co-Authors

A. Bogetti· 1 shared A. Brace· 1 shared A. C. Dommer· 1 shared A. Ramanathan· 1 shared A. Stern· 1 shared A. Trifan· 1 shared D. Hardy· 1 shared D. R. Roe· 1 shared

Activity by Year

2020-2024 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 28 mutual co-author links

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1 shared paperBiophysics

A. Bogetti

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3 papers

Recent·Most cited

k-Means NANI: an improved clustering algorithm for Molecular Dynamics simulations

L. Chen, D. R. Roe, M. Kochert, C. Simmerling, R. A. Miranda Quintana

The paper introduces NANI, a deterministic k-means clustering algorithm for molecular dynamics simulations that improves cluster accuracy and reproducibility compared to k-means++.

bioRxiv · Mar 7, 2024Biophysics

SpikeScape: A Tool for Analyzing Structural Diversity in Experimental Structures of the SARS-CoV-2 Spike Glycoprotein

D. Stepanenko, C. Simmerling

SpikeScape analyzes structural diversity in SARS-CoV-2 spike glycoprotein structures by standardizing data and calculating atom distance distributions across PDB entries.

bioRxiv · Nov 15, 2022Biophysics

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