Wolfram Liebermeister
Wolfram Liebermeister

Domaine de Vilvert
78352 Jouy-en-Josas, France
Charité Berlin - Institut für Biochemie
Charitéplatz 1
10117 Berlin, Germany
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DFG-funded research project "Dynamics and function of enzyme regulation in large metabolic networks"
Models and data

Metabolic network models

Bacillus subtilis (central metabolism model built from KEGG reaction IDs) [SBML] [SBtab]
Escherichia coli (central metabolism model built from KEGG reaction IDs) [SBML] [SBtab]
Human hepatocyte (adapted from original model provided by A. Hoppe) [SBtab]
Lactococcus lactis (adapted from original model provided by D. Bellomo) [SBtab]
Saccharomyces cerevisiae (central metabolism model built from KEGG reaction IDs) [SBML] [SBtab]

The format SBtab for data and models was developed within the project.

Data used for model building

Thermodynamic data
Standard Gibbs free energies (provided by E. Noor) [SBtab]

Protein sizes (number or amino acids)
[Bacillus subtilis] [Escherichia coli] [Saccharomyces cerevisiae]

Kinetic constants (collected from the Brenda database)
[Bacillus subtilis] [Escherichia coli] [Saccharomyces cerevisiae]

Metabolite concentrations
Bacillus subtilis(Buescher et al., 2012) [SBtab]
Escherichia coli(Bennet et al. 2009 and other sources) [SBtab]
Escherichia coli(Tepper et al., 2013) [SBtab]
Saccharomyces cerevisiae(Albe et al., 1990) [SBtab]

Protein abundances
Bacillus subtilis(Maass et al.) [SBtab]
Escherichia coli(Arike et al., 2012) [SBtab]
Escherichia coli(Lu et al., 2007) [SBtab]
Escherichia coli(Valgepea et al., 2013) [SBtab]
Saccharomyces cerevisiae(Nagaraj et al., 2012) [SBtab]

Metabolic fluxes
Bacillus subtilis(Kleijn et al., 2011) [SBtab]
Escherichia coli(Chen et al., 2010) [SBtab]
Saccharomyces cerevisiae(Christen et al., 2011) [SBtab]

Models and data accompanying the model construction methods developed in this project

Parameter balancing Example models
Enzyme cost minimisation E. coli model
Elasticity sampling Structural thermokinetic modelling
Model embedding Example models
Optimal enzyme oscillations Pathway models   |   Other models
Yeast metabolic oscillations Yeast model