Dataset Information

REME: an integrated platform for reaction enzyme mining and evaluation.

ABSTRACT: A key challenge in pathway design is finding proper enzymes that can be engineered to catalyze a non-natural reaction. Although existing tools can identify potential enzymes based on similar reactions, these tools encounter several issues. Firstly, the calculated similar reactions may not even have the same reaction type. Secondly, the associated enzymes are often numerous and identifying the most promising candidate enzymes is difficult due to the lack of data for evaluation. Thirdly, existing web tools do not provide interactive functions that enable users to fine-tune results based on their expertise. Here, we present REME (https://reme.biodesign.ac.cn/), the first integrated web platform for reaction enzyme mining and evaluation. Combining atom-to-atom mapping, atom type change identification, and reaction similarity calculation enables quick ranking and visualization of reactions similar to an objective non-natural reaction. Additional functionality enables users to filter similar reactions by their specified functional groups and candidate enzymes can be further filtered (e.g. by organisms) or expanded by Enzyme Commission number (EC) or sequence homology. Afterward, enzyme attributes (such as kcat, Km, optimal temperature and pH) can be assessed with deep learning-based methods, facilitating the swift identification of potential enzymes that can catalyze the non-natural reaction.

SUBMITTER: Shi Z

PROVIDER: S-EPMC11223788 | biostudies-literature | 2024 Jul

REPOSITORIES: biostudies-literature

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REME: an integrated platform for reaction enzyme mining and evaluation.

Shi Zhenkun Z Wang Dehang D Li Yang Y Deng Rui R Lin Jiawei J Liu Cui C Li Haoran H Wang Ruoyu R Zhao Muqiang M Mao Zhitao Z Yuan Qianqian Q Liao Xiaoping X Ma Hongwu H

Nucleic acids research 20240701 W1

A key challenge in pathway design is finding proper enzymes that can be engineered to catalyze a non-natural reaction. Although existing tools can identify potential enzymes based on similar reactions, these tools encounter several issues. Firstly, the calculated similar reactions may not even have the same reaction type. Secondly, the associated enzymes are often numerous and identifying the most promising candidate enzymes is difficult due to the lack of data for evaluation. Thirdly, existing ...[more]

PMID: 38769057

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Dataset Information

REME: an integrated platform for reaction enzyme mining and evaluation.

Publications

REME: an integrated platform for reaction enzyme mining and evaluation.

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