Author

A. Y. Shaw

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· 1 Bioengineering· 1 Pharmacology & Toxicology· 1

Signature Assays, Organisms & Methods

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Approach:deep learning· 2 Assay:protein sequence· 2 Research Focus:sequence-to-function modeling· 2 Research Focus:benchmarking· 1 Approach:large language model· 1 Approach:machine learning (classical)· 1 Research Focus:protein design· 1 Research Focus:protein folding & dynamics· 1

Frequent Co-Authors

D. S. Marks· 2 shared A. Kruse· 1 shared A. Wellner· 1 shared C. C. Liu· 1 shared C. Sander· 1 shared D. Ding· 1 shared D. Marks· 1 shared D. Savage· 1 shared

Activity by Year

2022-2023 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 19 mutual co-author links

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2 shared papersBioengineering

D. S. Marks

Mutual co-authors in cluster

Author profile →

3 papers

Recent·Most cited

Machine learning prediction of enzyme optimum pH

J. E. Gado, M. Knotts, A. Y. Shaw, D. Marks, N. P. Gauthier, C. Sander, G. T. Beckham

This study develops and evaluates machine learning models to predict enzyme optimum pH, finding that language model embeddings significantly improve prediction accuracy, leading to the release of the EpHod model.

bioRxiv · Jun 22, 2023Biochemistry

Protein design using structure-based residue preferences

D. Ding, A. Y. Shaw, S. Sinai, N. J. Rollins, N. Prywes, D. Savage, M. T. Laub, D. S. Marks

This paper introduces a method to design functional proteins using residue preferences derived from structural data, showing high accuracy in predicting combinatorial mutation effects.

bioRxiv · Oct 31, 2022Bioengineering

An in silico method to assess antibody fragment polyreactivity

E. P. Harvey, J.-E. Shin, M. A. Skiba, G. R. Nemeth, J. D. Hurley, A. Wellner, A. Y. Shaw, V. G. Miranda, J. K. Min, C. C. Liu, D. S. Marks, A. Kruse

The paper develops a machine learning model to assess and reduce polyreactivity in nanobody sequences, achieving high accuracy and practical application through a web server.

bioRxiv · Jan 12, 2022 · PreprintPharmacology & Toxicology