Author

Sonya Lee

University of California, San Francisco

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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Bioengineering· 1 Biophysics· 1

Signature Assays, Organisms & Methods

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Research Focus:protein structure prediction· 2 Organism:bacteria (other)· 1 Approach:deep learning· 1 Approach:diffusion model· 1 Research Focus:drug response / drug discovery· 1 Approach:experimental assay· 1 Research Focus:protein design· 1 Assay:protein structure· 1

Frequent Co-Authors

James S. FraseriD· 2 shared Artem Y. LyubimoviD· 1 shared Bo HuangiD· 1 shared Christian M. MacDonald· 1 shared Giuseppe Cimicata· 1 shared Guoxun ZhangiD· 1 shared Ian B. SeipleiD· 1 shared Klaus YserentantiD· 1 shared

Activity by Year

2025-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 27 mutual co-author links

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2 shared papersBioengineering

James S. FraserORCID

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2 papers

Recent·Most cited

Programming protein shape as an explicit design layer via CAD blueprint-guided diffusion

Yilun Qi, Guoxun Zhang, Klaus Yserentant, Sonya Lee, Artem Y. Lyubimov, Kyrellos E. Ibrahim, Giuseppe Cimicata, James S. Fraser, Bo Huang, Tanja Kortemme

The paper integrates CAD blueprints with diffusion models to explicitly program protein shapes, demonstrating emergent functions through molecular design.

bioRxiv · Jul 23, 2026 · PreprintBioengineering

Initial leads to combat streptogramin resistance generated from X-ray fragment screening against VatD

Pooja Asthana, Sonya Lee, Christian M. MacDonald, Ian B. Seiple, James S. Fraser

This study identifies fragment-based inhibitors of VatD, an enzyme responsible for streptogramin resistance, using X-ray crystallography to guide inhibitor development.

Structure · Sep 13, 2025Peer-reviewedBiophysics