Author

Samer F. Halabiya

University of Washington

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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Biochemistry· 2 Bioinformatics· 1 Synthetic Biology· 1

Signature Assays, Organisms & Methods

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Assay:protein structure· 3 Research Focus:drug response / drug discovery· 2 Approach:experimental assay· 2 Approach:deep learning· 1 Approach:machine learning (classical)· 1 Research Focus:protein design· 1 Research Focus:protein folding & dynamics· 1

Frequent Co-Authors

David A. BakeriD· 3 shared Brian CoventryiD· 2 shared Buwei HuangiD· 2 shared Cameron Cordray· 2 shared Inna GoreshnikiD· 2 shared Lance J. StewartiD· 2 shared Longxing CaoiD· 2 shared A. N. MurrayiD· 1 shared

Activity by Year

2021-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 35 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

Using experimental results of protein design to guide biomolecular energy-function development

Hugh K. Haddox, Gabriel J. Rocklin, Francis C. Motta, Devin Strickland, Samer F. Halabiya, Cameron Cordray, Hahnbeom Park, Eric Klavins, David A. Baker, Frank DiMaio

The paper uses experimental results from de novo protein designs to identify and resolve failure modes in the Rosetta energy function, improving its accuracy in predicting stable protein structures.

PLoS Computational Biology · Apr 22, 2026Peer-reviewedBiochemistry

Design of High Affinity Binders to Convex Protein Target Sites

David A. Baker, Wei Yang, Derrick R. Hicks, Agnidipta Ghosh, Tristin A. Schwartze, Brian Coventry, Inna Goreshnik, Aza Allen, Samer F. Halabiya, ChanJohng Kim, Cynthia S. Hinck, David S. Lee, Asim K. Bera, Zhe Li, Yujia Wang, , Andrew P. Hinck

This paper designs high-affinity proteins that bind to convex protein sites using geometrically matching concave scaffolds, achieving low nanomolar to picomolar affinities.

bioRxiv · May 1, 2024 · PreprintBiochemistry

High-throughput ML-guided design of diverse single-domain antibodies against SARS-CoV-2

Christof Angermueller, Zelda Mariet, Benjamin W. Jester, Emily Engelhart, Ryan Emerson, Babak Alipanahi, Charles Lin, Colleen Shikany, Daniel Guion, Joel B. Nelson, Mary Kelley, Margot McMurray, Parker Shaffer, Cameron Cordray, Samer F. Halabiya, , Lucy J. Colwell

This study uses ML to design diverse VHH antibodies that neutralize SARS-CoV-1 and SARS-CoV-2 variants, including Delta and Omicron BA.1.

bioRxiv · Dec 1, 2023 · PreprintBioinformatics

Robust de novo design of protein binding proteins from target structural information alone

Longxing Cao, Brian Coventry, Inna Goreshnik, Buwei Huang, Joon Sung Park, Kevin M. Jude, Iva Marković, Rameshwar U. Kadam, Koen H. G. Verschueren, Kenneth Verstraete, Scott Thomas Russell Walsh, Nathaniel R. Bennett, Ashish Phal, Aerin Yang, Lisa Kozodoy, , David A. Baker

This paper designs small, stable proteins that bind to diverse target proteins using only structural information, achieving nanomolar to picomolar affinities.

bioRxiv · Sep 4, 2021 · PreprintSynthetic Biology