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Modeling, predicting and mining metabolism at atom-level resolution

Publications associées (128)

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In the beginning was the metabolism. The biochemical processes that make life possible transformed the soup of chemicals into the life on Earth we know today. Since then, living organisms have evolved, and life on Earth has become more complex. Living orga ...

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Generative machine learning produces kinetic models that accurately characterize intracellular metabolic states

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Large omics datasets are nowadays routinely generated to provide insights into cellular processes. Nevertheless, making sense of omics data and determining intracellular metabolic states remains challenging. Kinetic models of metabolism are crucial for int ...

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An explainability framework for deep learning on chemical reactions exemplified by enzyme-catalysed reaction classification

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Assigning or proposing a catalysing enzyme given a chemical or biochemical reaction is of great interest to life sciences and chemistry alike. The exploration and design of metabolic pathways and the challenge of finding more sustainable enzyme-catalysed a ...

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The metabolic engineering community relies on computational methods for pathway design to produce important small molecules in microbial hosts. Metabolic network databases are continuously curated and updated with known and novel reactions that expand the ...

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Metabolic "dark matter" describes currently unknown metabolic processes, which form a blind spot in our general understanding of metabolism and slow down the development of biosynthetic cell factories and naturally derived pharmaceuticals. Mapping the dark ...

NATURE PORTFOLIO2022

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In the biosynthesis of the iron-guanylylpyridinol (FeGP) cofactor, 6-carboxymethyl-5-methyl-4-hydroxy-2-pyridinol (1) is 3-methylated to form 2, then 4-guanylylated to form 3, and converted into the full cofactor. HcgA-G proteins catalyze the biosynthetic ...

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Assessment of metal-based dihydrofolate reductase inhibitors on a novel mesofluidic platform

Paul Joseph Dyson, Sarah Alexandra Pais Pereira

A new miniaturized micro sequential injection coupled with the lab-on-valve (mu SIA-LOV) technique was full-blown to perform inhibitory studies on dihydrofolate reductase (DHFR). The system was used to evaluate the DHFR inhibition activity of metal-based a ...

ELSEVIER SCIENCE SA2022

Motivation: Finding biosynthetic pathways is essential for metabolic engineering of organisms to produce chemicals, biodegradation prediction of pollutants and drugs, and for the elucidation of bioproduction pathways of secondary metabolites. A key step in ...

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