Comprehensive Machine Learning Prediction of Extensive Enzymatic Reactions

• Published in: The journal of physical chemistry. B 2022-09, Vol.126 (36), p.6762-6770
• Main Authors: Watanabe, Naoki, Yamamoto, Masaki, Murata, Masahiro, Vavricka, Christopher J., Ogino, Chiaki, Kondo, Akihiko, Araki, Michihiro
• Format: Article
• Language: English
• Subjects: biosynthesis; enzymatic reactions; enzymes; neural networks; physical chemistry; prediction
• ISSN: 1520-6106; 1520-5207; 1520-5207
• DOI: 10.1021/acs.jpcb.2c03287

New enzyme functions exist within the increasing number of unannotated protein sequences. Novel enzyme discovery is necessary to expand the pathways that can be accessed by metabolic engineering for the biosynthesis of functional compounds. Accordingly, various machine learning models have been developed to predict enzymatic reactions. However, the ability to predict unknown reactions that are not included in the training data has not been clarified. In order to cover uncertain and unknown reactions, a wider range of reaction types must be demonstrated by the models. Here, we establish 16 expanded enzymatic reaction prediction models developed using various machine learning algorithms, including deep neural network. Improvements in prediction performances over that of our previous study indicate that the updated methods are more effective for the prediction of enzymatic reactions. Overall, the deep neural network model trained with combined substrate–enzyme–product information exhibits the highest prediction accuracy with Macro F₁ scores up to 0.966 and with robust prediction of unknown enzymatic reactions that are not included in the training data. This model can predict more extensive enzymatic reactions in comparison to previously reported models. This study will facilitate the discovery of new enzymes for the production of useful substances.