The Classification of Enzymes by Deep Learning

Zhiyu Tao,Yuming Zhao,Zhixia Teng,Benzhi Dong

doi:10.1109/access.2020.2992468

Zhiyu Tao, Yuming Zhao + Show 2 more

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https://doi.org/10.1109/access.2020.2992468

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Abstract

Enzymes, as a group of crucial biocatalysts produced by living cells, enable the chemical reactions in organisms to be more efficient. According to the properties of the reactions catalyzed by enzymes, the Enzyme Commission (EC) number system divided enzymes into 6 primary main classes in 1961: oxidoreductases (EC1), transferases (EC2), hydrolases (EC3), lyases (EC4), isomerases (EC5), and ligases (EC6). These six categories did not change for many years until a new class, the translocases (EC7), was added in August 2018. Different enzymes have different properties of catalytic reaction, and the prediction of enzyme classes is a very important research topic, allowing us to further study the structure and function of enzyme molecules when we know the category of enzyme. Because the number of enzymes whose function remains unknown is enormous, it is time-consuming to use biological experiments to determine enzyme characteristics. Thus, devising various computational models to predict enzyme classes has become a feasible scheme. In hope of giving researchers more inspiration and ideas for predicting the EC number of enzymes by machine learning, we summarize a variety of research methods used in the prediction of enzyme families in this research.

Highlights

As a type of very important biocatalyst, enzymes have a vital role in maintaining the life activities of organisms
To facilitate research for scholars in this field, we summarize some recent machine learning methods utilized in predicting enzyme classes that are novel and classic
In the second and third parts, we introduce some methods adopted in the latest papers or used frequently for feature extraction and classification

Summary

Introduction

As a type of very important biocatalyst, enzymes have a vital role in maintaining the life activities of organisms. They dominate the metabolism, nutrition, energy conversion and many other chemical reactions closely related to the life process. The Commission has classified enzymes into 7 main classes. Most classifiers designed by scholars can classify enzymes to the level of subclass [1]–[3].

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Conclusion