A review of computational tools for design and reconstruction of metabolic pathways

L Wang, S Dash, CY Ng, CD Maranas - Synthetic and systems …, 2017 - Elsevier
Metabolic pathways reflect an organism's chemical repertoire and hence their elucidation
and design have been a primary goal in metabolic engineering. Various computational …

High efficient production of plant flavonoids by microbial cell factories: Challenges and opportunities

J Sun, W Sun, G Zhang, B Lv, C Li - Metabolic engineering, 2022 - Elsevier
Plant flavonoids are secondary metabolites containing a benzo-γ-pyrone structure, which
are widely present in plants and have a variety of physiological and pharmacological …

Discovery of toxin-degrading enzymes with positive unlabeled deep learning

D Zhang, H **ng, D Liu, M Han, P Cai, H Lin, Y Tian… - Acs …, 2024 - ACS Publications
Identifying functional enzymes for the catalysis of specific biochemical reactions is a major
bottleneck in the de novo design of biosynthesis and biodegradation pathways …

Enzyme annotation for orphan and novel reactions using knowledge of substrate reactive sites

N Hadadi, H MohammadiPeyhani, L Miskovic… - Proceedings of the …, 2019 - pnas.org
Thousands of biochemical reactions with characterized activities are “orphan,” meaning they
cannot be assigned to a specific enzyme, leaving gaps in metabolic pathways. Novel …

Data-driven prediction of molecular biotransformations in food fermentation

D Zhang, C Jia, D Sun, C Gao, D Fu… - Journal of Agricultural …, 2023 - ACS Publications
Fermentation products, together with food components, determine the sense, nutrition, and
safety of fermented foods. Traditional methods of fermentation product identification are time …

novoPathFinder: a webserver of designing novel-pathway with integrating GEM-model

S Ding, Y Tian, P Cai, D Zhang, X Cheng… - Nucleic acids …, 2020 - academic.oup.com
To increase the number of value-added chemicals that can be produced by metabolic
engineering and synthetic biology, constructing metabolic space with novel …

Methylglucosylation of aromatic amino and phenolic moieties of drug-like biosynthons by combinatorial biosynthesis

L **e, L Zhang, C Wang, X Wang, Y Xu, H Yu… - Proceedings of the …, 2018 - pnas.org
Glycosylation is a prominent strategy to optimize the pharmacokinetic and
pharmacodynamic properties of drug-like small-molecule scaffolds by modulating their …

A systems approach to predict oncometabolites via context-specific genome-scale metabolic networks

H Nam, M Campodonico, A Bordbar… - PLoS computational …, 2014 - journals.plos.org
Altered metabolism in cancer cells has been viewed as a passive response required for a
malignant transformation. However, this view has changed through the recently described …

MycotoxinDB: A data-driven platform for investigating masked forms of mycotoxins

J Ji, D Zhang, J Ye, Y Zheng, J Cui… - Journal of Agricultural …, 2023 - ACS Publications
Mycotoxins are likely to be converted into masked forms when subjected to plant metabolism
or food processing. These masked forms of mycotoxins together with their prototypes may …

Bottom-up synthetic biology approach for improving the efficiency of menaquinone-7 synthesis in Bacillus subtilis

X Ding, Z Zheng, G Zhao, L Wang, H Wang… - Microbial Cell …, 2022 - Springer
Abstract Background Menaquinone-7 (MK-7), which is associated with complex and tightly
regulated pathways and redox imbalances, is produced at low titres in Bacillus subtilis …