EnzyKR: a chirality-aware deep learning model for predicting the outcomes of the hydrolase-catalyzed kinetic resolution
Open accessPublished version of a preprint
Abstract
EnzyKR is designed to guide the identification of hydrolase scaffolds for resolving a racemic substrate mixture for stereoselective synthesis.
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Cites
Evolutionary-scale prediction of atomic level protein structure with a language model
Lin, Z., Akin, H., Rao, R., Hie, B., Zhu, Z., Lu, W., Smetanin, N., Verkuil, R., Kabeli, O., Shmueli, Y., et al. (2022) · doi:10.1101/2022.07.20.500902 · Cited by 5,523 · see citing works
Deep learning-based kcat prediction enables improved enzyme-constrained model reconstruction
Li, F., Yuan, L., Lu, H., Li, G., Chen, Y., Engqvist, M. K. M., Kerkhoven, E. J., & Nielsen, J. (2022) · Nature Catalysis · doi:10.1038/s41929-022-00798-z · Cited by 466 · cited 4× · see citing works
“This also outperforms DLKcat, which shows a lower recall of 0.39.”
BackgroundMethodInfluentialMachine learning modeling of family wide enzyme-substrate specificity screens
Goldman, S., Das, R., Yang, K. K., & Coley, C. W. (2022) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1009853 · Cited by 120 · see citing works
Mutexa: A Computational Ecosystem for Intelligent Protein Engineering
Yang, Z. J., Shao, Q., Jiang, Y., Jurich, C., Ran, X., Juarez, R. J., Yan, B., Stull, S. L., Gollu, A., & Ding, N. (2023) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.3c00602 · Cited by 28 · see citing works
Self-citation
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Sorted by citations
Protein representations: Encoding biological information for machine learning in biocatalysis
Harding-Larsen, D., Funk, J., Madsen, N. G., Gharabli, H., Acevedo-Rocha, C. G., Mazurenko, S., & Welner, D. H. (2024) · Biotechnology Advances · doi:10.1016/j.biotechadv.2024.108459 · Cited by 38 · see citing works
Mutexa: A Computational Ecosystem for Intelligent Protein Engineering
Yang, Z. J., Shao, Q., Jiang, Y., Jurich, C., Ran, X., Juarez, R. J., Yan, B., Stull, S. L., Gollu, A., & Ding, N. (2023) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.3c00602 · Cited by 28 · see citing works
Self-citationFinding the dark matter: Large language model‐based enzyme kinetic data extractor and its validation
Wei, G., Ran, X., AI‐Abssi, R., & Yang, Z. (2025) · Protein Science · doi:10.1002/pro.70251 · Cited by 10 · see citing works
Self-citation
- Authors
- Ran, X., Jiang, Y., Shao, Q., & Yang, Z. J.
- Affiliations
- Vanderbilt University (US)
- Corresponding author
- Yang, Zhongyue J.
- Venue
- Chemical Science
- Publisher
- Royal Society of Chemistry (RSC)
- Published
- 2023
- Volume
- 14
- Issue
- 43
- Pages
- 12073-12082
- ISSN
- 2041-6520 (ISSN-L)
- 2041-6539
- PMC
- PMC10631226
- OpenAlex
- W4387693468
- Cited by
- 25
- References
- 4
- Citations by year
- 2026: 9 · 2025: 7 · 2024: 7 · 2023: 2
- FWCI
- 2.23
- Type
- journal article
- Language
- en
- Open access
- diamond
- doi.org
- Licence
- Locations
- Chemical Science (publishedVersion, cc-by-nc)
- ChemRxiv (acceptedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- eScholarship (California Digital Library) (submittedVersion, cc-by-nc)
- Funders
- Vanderbilt University
- National Institute of General Medical Sciences
- National Institutes of Health (R35GM146982)
- National Science Foundation (BIO200057)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Enzyme Catalysis and Immobilization
- Physical Sciences › Chemistry › Organic Chemistry › Asymmetric Synthesis and Catalysis
- Physical Sciences › Chemistry › Organic Chemistry › Chemical Reaction Mechanisms
- Keywords
- kinetic resolution, esterase, chiral biocatalysis
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