Models

What is a Model?
418 Models visible to you, out of a total of 662
No description specified

Creators: Dawie van Niekerk, Jacky Snoep

Submitter: Dawie van Niekerk

A reconstruction of the cellular metabolism of the opportunistic human pathogen Enterococcus faecalis V583 represented as stoichiometric model and analysed using constraint-based modelling approaches

Glycolytic model for Plasmodium falciparum; open system

Creators: Dawie van Niekerk, Jacky Snoep

Submitter: Dawie van Niekerk

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

Creators: Dawie van Niekerk, Jacky Snoep

Submitter: Dawie van Niekerk

Glycolytic model for Plasmodium falciparum; closed system

Creators: Dawie van Niekerk, Jacky Snoep

Submitter: Dawie van Niekerk

Mathematica notebook for the parameterisation of the G3PDH rate equation based on SEEK linked experimental data.

Creators: Dawie van Niekerk, Jacky Snoep

Submitter: Dawie van Niekerk

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

Creators: Dawie van Niekerk, Jacky Snoep

Submitter: Dawie van Niekerk

Mathematica notebook for the ATPase reaction.

Creators: Dawie van Niekerk, Jacky Snoep

Submitter: Dawie van Niekerk

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

Creators: Dawie van Niekerk, Jacky Snoep

Submitter: Dawie van Niekerk

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

Creators: Dawie van Niekerk, Jacky Snoep

Submitter: Dawie van Niekerk

Mathematica notebook for the glycerol transport rate equation.

Creators: Dawie van Niekerk, Jacky Snoep

Submitter: Dawie van Niekerk

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

Creators: Dawie van Niekerk, Jacky Snoep

Submitter: 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

Submitter: Dawie van Niekerk

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

Creators: Dawie van Niekerk, Jacky Snoep

Submitter: Dawie van Niekerk

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

Creators: Dawie van Niekerk, Jacky Snoep

Submitter: Dawie van Niekerk

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

Creators: Dawie van Niekerk, Jacky Snoep

Submitter: Dawie van Niekerk

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

Creators: Dawie van Niekerk, Jacky Snoep

Submitter: Dawie van Niekerk

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

Creators: Dawie van Niekerk, Jacky Snoep

Submitter: Dawie van Niekerk

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

Creators: Dawie van Niekerk, Jacky Snoep

Submitter: 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

Submitter: Dawie van Niekerk

Mathematical model for HK kinetics, GLC and ATP saturation, and inhibition with G6P and ADP.

Creators: Dawie van Niekerk, Jacky Snoep

Submitter: Dawie van Niekerk

Mechanistical model of the catalytic cycle of Trypanothione Synthetase

Creators: Jurgen Haanstra, Alejandro Leroux

Submitter: Jurgen Haanstra

An ODE model of the gene regulation network governing sporulation initiation in Bacillus subtilis to be run in Matlab.

The network incorporates four sporulation-related signals: nutrient supply, DNA damage, the products of the competence genes and the bacterial population size.

Run execute_bacillus_sporulation_initiation.m to simulate the model. This file also contains the signal-related parameters which can be altered to investigate the effect of competing signals.

Some results for this model ...

Creator: Sara Jabbari

Submitter: Sara Jabbari

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

This function estimates the parameters of growth functions of the acid-forming and solvent-forming population observed in 'forward'-shift experiments of phosphate-limited continuous cultures of C. acetobutylicum. The parameters are used in the 'Two-Populations'-Model of the pH-induced metabolic shift.

It assumed that the found behaviour of the optical density during these experiments results from a phenotypic switch caused by the changing pH level.

Creator: Thomas Millat

Submitter: 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

Submitter: 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

Submitter: 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

Submitter: 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

Submitter: 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¬AS,threshold and ECS,threshold, respectively. For the other LDH enzymes, ...

Creator: Anna Feldman-Salit

Submitter: Anna Feldman-Salit

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