Models

118 Models visible to you, out of a total of 194

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
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Creator: Thomas Millat

Contributor: Thomas Millat

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

Contributor: Anna Feldman-Salit

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

Contributor: Anna Feldman-Salit

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

Contributor: Anna Feldman-Salit

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

Contributor: Anna Feldman-Salit

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┬ČAS,threshold and ECS,threshold, respectively. For the other LDH enzymes,
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Creator: Anna Feldman-Salit

Contributor: Anna Feldman-Salit

This partial-differential equations model focuses on the oxygen gradients in consideration of the three-dimensional cell and environment.

Creator: Samantha Nolan

Contributor: David Knies

Mathematica notebook for the parameterisation of the PFK rate equation based on SEEK linked experimental data.

Creators: Dawie Van Niekerk, Jacky Snoep

Contributor: Dawie Van Niekerk

Mathematica notebook for the parameterisation of the PGI rate equation based on SEEK linked experimental data.

Creators: Dawie Van Niekerk, Jacky Snoep

Contributor: Dawie Van Niekerk

Mathematical model for PGK kinetics, ADP, ATP, 3PG and BPG saturation.

Creator: Jacky Snoep

Contributor: Jacky Snoep

Mathematica notebook for the parameterisation of the PGK rate equation based on SEEK linked experimental data.

Creators: Dawie Van Niekerk, Jacky Snoep

Contributor: Dawie Van Niekerk

Mathematica notebook for the parameterisation of the PGM rate equation based on SEEK linked experimental data.

Creators: Dawie Van Niekerk, Jacky Snoep

Contributor: Dawie Van Niekerk

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

Contributor: Thomas Millat

Mathematica notebook for the parameterisation of the PK rate equation based on the experimental SEEK data set

Creators: Dawie Van Niekerk, Jacky Snoep

Contributor: Dawie Van Niekerk

No description specified

Creator: Paul Heusden

Contributor: JERM

The kinetic model includes sugar uptake, degradation of glucose into pyruvate and the fermentation of pyruvate.

Creators: Jennifer Levering, Mark Musters

Contributor: Jennifer Levering

The kinetic model includes sugar uptake, degradation of glucose into pyruvate and the fermentation of pyruvate.

Creator: Jennifer Levering

Contributor: Jennifer Levering

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

Contributor: Nadine Veith

Mathematica notebook for the pyruvate transport rate equation, based on literature data.

Creators: Dawie Van Niekerk, Jacky Snoep

Contributor: Dawie Van Niekerk

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