Models
What is a Model?Filters
The fitted function describes the pH-drop during 'forward'-shift experiments and the increase of the pH during 'reverse'-shift experiments. The estimated parameters are used to compute the changing pH level in the models of the pH.induced metabolic shift in continuous cultures under phosphate limitation of C. acetobutylicum. Furthermore, the parameters can be applied to join different independent experiments into a single data set.
To fit the changing pH level, an exponential function and a ...
Creator: Thomas Millat
Submitter: Thomas Millat
Model type: Not specified
Model format: Matlab package
Environment: Matlab
3D structure prediction of LDH enzymes from four LAB by comparative modeling against x-ray structure of LDH from B. stearothermophilis (template, PDB ID: 1LDN). The computation was performed with a protocol that uses "automodel.very_fast" settings of Modeller program (http://salilab.org/modeller/).
Creator: Anna Feldman-Salit
Submitter: Anna Feldman-Salit
Model type: Not specified
Model format: Not specified
Environment: Not specified
Computation is performed for the modeled 3D structures of LDH enzymes (in PDB format) with the UHBD program, for pH 6 and pH 7.
Creator: Anna Feldman-Salit
Submitter: Anna Feldman-Salit
Model type: Not specified
Model format: Not specified
Environment: Not specified
Comparison of electrostatic potentials within the allosteric binding sites of LDH enzymes to estimate the binding affinity of the FBP molecule is performed with the PIPSA program. The program uses the structure of enzymes in the PDB format and computed electrostatic potentials in the GRD format.
Creator: Anna Feldman-Salit
Submitter: Anna Feldman-Salit
Model type: Not specified
Model format: Not specified
Environment: Not specified
Binding energies of phosphate ions to the allosteric and catalytic sites were estimated with a program GRID (http://www.moldiscovery.com/soft_grid.php). The calculations were performed for the modeled LDH structures from four LABs, at pH 6 and 7, in presence and absence of the FBP molecule. The phosphate ion was presented as a probe.
Creator: Anna Feldman-Salit
Submitter: Anna Feldman-Salit
Model type: Not specified
Model format: Not specified
Environment: Not specified
In order to estimate whether Pi has an activatory or an inhibitory effect on the enzymes, the computed probe binding energies (from GRID results, Part 4) were compared with those for the LDH from L. plantarum whose activity is known to be unaffected by Pi.
The binding energies of the Pi probe in the allosteric binding site (AS) and the COO probe in the catalytic binding site (CS) of LDH from L. plantarum were defined as E¬AS,threshold and ECS,threshold, respectively. For the other LDH enzymes, ...
Creator: Anna Feldman-Salit
Submitter: Anna Feldman-Salit
Model type: Algebraic equations
Model format: Not specified
Environment: Not specified
This partial-differential equations model focuses on the oxygen gradients in consideration of the three-dimensional cell and environment.
Creator: Samantha Nolan
Submitter: David Knies
Model type: Partial differential equations (PDE)
Model format: Mathematica
Environment: Not specified
PGK model for S. solfataricus
Creator: Jacky Snoep
Submitter: Jacky Snoep
Model type: Algebraic equations
Model format: Mathematica
Environment: Mathematica
PGK 70C SBML
Creator: Jacky Snoep
Submitter: Jacky Snoep
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Mathematical model for PGK kinetics, ADP, ATP, 3PG and BPG saturation.
Creator: Jacky Snoep
Submitter: Jacky Snoep
Model type: Ordinary differential equations (ODE)
Model format: Mathematica
Environment: Not specified
PGK yeast Fig1a
Creator: Jacky Snoep
Submitter: Jacky Snoep
Model type: Ordinary differential equations (ODE)
Model format: Mathematica
Environment: Mathematica
PGK yeast with/without recycling
Creator: Jacky Snoep
Submitter: Jacky Snoep
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
PGK-GAPDH model Sulfolobus kouril8
Creator: Jacky Snoep
Submitter: Jacky Snoep
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
PGK-GAPDH model yeast kouril7
Creator: Jacky Snoep
Submitter: Jacky Snoep
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
PGK-GAPDH models yeast and Sulfolobus Fig. 4 in manuscript
Creator: Jacky Snoep
Submitter: Jacky Snoep
Model type: Ordinary differential equations (ODE)
Model format: Mathematica
Environment: Mathematica
Here, we use hyperbolic tangents to fit experimental data of AB fermentation in C. acetobutylicum in continous culture at steady state for different external pHs. The estimated parameters are used to define acidogenic and solventogenic phase. Furthermore, an transition phase is identified which cannot be assigned to acidogenesis or solventogenesis.
Several plots compare the fits to the experimental data.
Creator: Thomas Millat
Submitter: Thomas Millat
Model type: Not specified
Model format: Matlab package
Environment: Matlab
Creator: Paul Heusden
Submitter: The JERM Harvester
Model type: Not specified
Model format: Not specified
Environment: Not specified
The kinetic model includes sugar uptake, degradation of glucose into pyruvate and the fermentation of pyruvate.
Creators: Jennifer Levering, Mark Musters
Submitter: Jennifer Levering
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
The kinetic model includes sugar uptake, degradation of glucose into pyruvate and the fermentation of pyruvate.
Creator: Jennifer Levering
Submitter: Jennifer Levering
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Structural models of the LAB PYKs of L. lactis, L. plantarum, S. pyogenes and E. faecalis including the "best" docking solutions of potential allosteric ligands. The structures were derived by homology modeling based on the template of E. coli and B. stearothermophilus. PYK models and ligands are provided as .pdb files and can be displayed by using the program PyMOL, for instance.
Creators: Nadine Veith, Anna Feldman-Salit, Stefan Henrich, Rebecca Wade
Submitter: Nadine Veith
Model type: Not specified
Model format: Not specified
Environment: Not specified