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Learning deep repre...
Learning deep representations of enzyme thermal adaptation
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- Li, Gang, 1991 (author)
- Chalmers tekniska högskola,Chalmers University of Technology
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- Buric, Filip, 1988 (author)
- Chalmers tekniska högskola,Chalmers University of Technology
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- Zrimec, Jan, 1981 (author)
- Chalmers tekniska högskola,Chalmers University of Technology
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- Viknander, Sandra, 1990 (author)
- Chalmers tekniska högskola,Chalmers University of Technology
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- Nielsen, Jens B, 1962 (author)
- BioInnovation Institute (BII),Chalmers tekniska högskola,Chalmers University of Technology
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- Zelezniak, Aleksej, 1984 (author)
- Chalmers tekniska högskola,Chalmers University of Technology,Vilniaus universitetas,Vilnius University
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- Engqvist, Martin, 1983 (author)
- Chalmers tekniska högskola,Chalmers University of Technology
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(creator_code:org_t)
- 2022-11-22
- 2022
- English.
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In: Protein Science. - : Wiley. - 1469-896X .- 0961-8368. ; 31:12
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https://research.cha...
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https://doi.org/10.1...
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Abstract
Subject headings
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- Temperature is a fundamental environmental factor that shapes the evolution of organisms. Learning thermal determinants of protein sequences in evolution thus has profound significance for basic biology, drug discovery, and protein engineering. Here, we use a data set of over 3 million BRENDA enzymes labeled with optimal growth temperatures (OGTs) of their source organisms to train a deep neural network model (DeepET). The protein-temperature representations learned by DeepET provide a temperature-related statistical summary of protein sequences and capture structural properties that affect thermal stability. For prediction of enzyme optimal catalytic temperatures and protein melting temperatures via a transfer learning approach, our DeepET model outperforms classical regression models trained on rationally designed features and other deep-learning-based representations. DeepET thus holds promise for understanding enzyme thermal adaptation and guiding the engineering of thermostable enzymes.
Subject headings
- NATURVETENSKAP -- Biologi -- Biokemi och molekylärbiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Biochemistry and Molecular Biology (hsv//eng)
- NATURVETENSKAP -- Data- och informationsvetenskap -- Bioinformatik (hsv//swe)
- NATURAL SCIENCES -- Computer and Information Sciences -- Bioinformatics (hsv//eng)
- NATURVETENSKAP -- Biologi -- Bioinformatik och systembiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Bioinformatics and Systems Biology (hsv//eng)
Keyword
- deep neural networks
- bioinformatics
- enzyme catalytic temperatures
- protein thermostability
- transfer learning
- optimal growth temperatures
Publication and Content Type
- art (subject category)
- ref (subject category)
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- By the author/editor
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Li, Gang, 1991
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Buric, Filip, 19 ...
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Zrimec, Jan, 198 ...
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Viknander, Sandr ...
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Nielsen, Jens B, ...
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Zelezniak, Aleks ...
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show more...
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Engqvist, Martin ...
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- About the subject
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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Biological Scien ...
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and Biochemistry and ...
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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Computer and Inf ...
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and Bioinformatics
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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Biological Scien ...
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and Bioinformatics a ...
- Articles in the publication
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Protein Science
- By the university
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Chalmers University of Technology