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

Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print Cited Medium: Internet ISSN: 1362-4962 (Electronic) Linking ISSN: 03051048 NLM ISO Abbreviation: Nucleic Acids Res Subsets: MEDLINE

Publication: 1992- : Oxford : Oxford University Press
Original Publication: London, Information Retrieval ltd.

Enzymes*/chemistry ; Enzymes*/metabolism ; Software*; Data Mining/methods ; Internet ; Deep Learning ; Biocatalysis

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.
(© The Author(s) 2024. Published by Oxford University Press on behalf of Nucleic Acids Research.)

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XDC0120201 Strategic Priority Research Program of the Chinese Academy of Sciences; 12326611 National Natural Science Foundation of China; TSBICIP-PTJS-001 Tianjin Synthetic Biotechnology Innovation Capacity Improvement; 22HHSWSS00021 Haihe Laboratory of Synthetic Biology

0 (Enzymes)

Date Created: 20240520 Date Completed: 20240704 Latest Revision: 20240706

20240706

PMC11223788

10.1093/nar/gkae405

38769057