Dynamic models for metabolomics data integration

Weindl, Daniel

doi:10.1016/j.coisb.2021.100358

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2022

2024

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Cited by 7 publications

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“…However, metabolic fluxes are not directly measurable and must be inferred through metabolic modeling. Besides constraint-based modeling [3], the most successful approaches are based on stable isotope labeling experiments [4,5]. Here, a stable isotope (mostly 13 C) labeled substrate is applied and the metabolization of this compound will lead to specific isotopic enrichment patterns in downstream metabolites.…”

Section: Introductionmentioning

confidence: 99%

MetAMDB: Metabolic Atom Mapping Database

Starke

Wegner

2022

Metabolites

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MetAMDB is an open-source metabolic atom mapping database, providing atom mappings for around 43,000 metabolic reactions. Each atom mapping can be inspected and downloaded either as an RXN file or as a graphic in SVG format. In addition, MetAMDB offers the possibility of automatically creating atom mapping models based on user-specified metabolic networks. These models can be of any size (small to genome-scale) and can subsequently be used in standard 13C metabolic flux analysis software.

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