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Related Experiment Video

Updated: Oct 2, 2025

Concentration of Metabolites from Low-density Planktonic Communities for Environmental Metabolomics using Nuclear Magnetic Resonance Spectroscopy
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Concentration of Metabolites from Low-density Planktonic Communities for Environmental Metabolomics using Nuclear Magnetic Resonance Spectroscopy

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MetAMDB: Metabolic Atom Mapping Database.

Collin Starke1, Andre Wegner1

  • 1Department of Bioinformatics and Biochemistry, Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106 Braunschweig, Germany.

Metabolites
|February 25, 2022
PubMed
Summary
This summary is machine-generated.

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MetAMDB is a new metabolic atom mapping database offering over 43,000 reaction mappings. This resource aids in 13C metabolic flux analysis by providing downloadable atom mapping models for metabolic networks.

Area of Science:

  • Metabolic Engineering
  • Systems Biology
  • Bioinformatics

Background:

  • Metabolic flux analysis (MFA) is crucial for understanding cellular metabolism.
  • Accurate atom mapping is essential for reliable MFA, particularly in 13C-MFA.
  • Existing resources for metabolic atom mapping are limited.

Purpose of the Study:

  • To introduce MetAMDB, an open-source database for metabolic atom mapping.
  • To provide comprehensive atom mappings for a large number of metabolic reactions.
  • To enable the creation of custom atom mapping models for diverse metabolic networks.

Main Methods:

  • Development of an open-source metabolic atom mapping database (MetAMDB).
  • Inclusion of approximately 43,000 metabolic reactions with atom mappings.
Keywords:
13C metabolic flux analysisAAMRXNatom mapping modelatom mappingsatom transitionsdatabasemetabolic modelsystems biochemistry

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  • Implementation of functionalities for inspecting and downloading atom mappings (RXN, SVG).
  • Development of automated model creation for user-specified metabolic networks.

    • Main Results:

    • MetAMDB provides atom mappings for ~43,000 metabolic reactions.
    • Atom mappings are accessible for download as RXN files or SVG graphics.
    • Automated generation of atom mapping models is supported for networks of any scale.
    • Generated models are compatible with standard 13C metabolic flux analysis software.

    Conclusions:

    • MetAMDB serves as a valuable, open-source resource for metabolic atom mapping.
    • The database facilitates 13C-MFA by providing accessible and customizable atom mapping models.
    • MetAMDB supports research in metabolic engineering and systems biology through enhanced data availability.