A deep learning approach to evaluate the feasibility of enzymatic reactions generated by retrobiosynthesis |
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Authors: | Yeji Kim Jae Yong Ryu Hyun Uk Kim Woo Dae Jang Sang Yup Lee |
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Affiliation: | 1. Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering, KAIST Institute for BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea;2. Data Convergence Drug Research Center, Korea Research Institute of Chemical Technology, Daejeon, Republic of Korea;3. Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, Daejeon, Republic of Korea |
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Abstract: | Retrobiosynthesis allows the designing of novel biosynthetic pathways for the production of chemicals and materials through metabolic engineering, but generates a large number of reactions beyond the experimental feasibility. Thus, an effective method that can reduce a large number of the initially predicted enzymatic reactions has been needed. Here, we present Deep learning-based Reaction Feasibility Checker (DeepRFC) to classify the feasibility of a given enzymatic reaction with high performance and speed. DeepRFC is designed to receive Simplified Molecular-Input Line-Entry System (SMILES) strings of a reactant pair, which is defined as a substrate and a product of a reaction, as an input, and evaluates whether the input reaction is feasible. A deep neural network is selected for DeepRFC as it leads to better classification performance than five other representative machine learning methods examined. For validation, the performance of DeepRFC is compared with another in-house reaction feasibility checker that uses the concept of reaction similarity. Finally, the use of DeepRFC is demonstrated for the retrobiosynthesis-based design of novel one-carbon assimilation pathways. DeepRFC will allow retrobiosynthesis to be more practical for metabolic engineering applications by efficiently screening a large number of retrobiosynthesis-derived enzymatic reactions. DeepRFC is freely available at https://bitbucket.org/kaistsystemsbiology/deeprfc . |
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Keywords: | deep learning DeepRFC enzymatic reaction reaction feasibility retrobiosynthesis |
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