Models

What is a Model?
418 Models visible to you, out of a total of 662

Model written in Antimony human-readable language, Model used in Pokhilko et al 2012

Creators: Uriel Urquiza Garcia, Andrew Millar

Submitter: Uriel Urquiza Garcia

Model written in Antimony human-readable language and then translate into SBML using Tellurium

Creators: Uriel Urquiza Garcia, Andrew Millar

Submitter: Uriel Urquiza Garcia

Exactly the same as model 243, but uploaded as a file rather than copied from PlaSMo.

Creator: Andrew Millar

Submitter: Andrew Millar

The P2011.3.1 SBML model imported into Copasi v4.8, saved as native Copasi file

Creators: Andrew Millar, Uriel Urquiza Garcia, Kevin Stratford, EPCC

Submitter: Andrew Millar

Arabidopsis clock model P2011.6.1 SBML imported into Copasi 4.8 and saved as native Copasi file.

Creators: Andrew Millar, Uriel Urquiza Garcia, Kevin Stratford, EPCC

Submitter: Andrew Millar

A diagram encoding PAMP signaling relevant to COVID-19/SARS-CoV-2

Creator: Matti Hoch

Submitter: Marek Ostaszewski

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

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

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

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

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

Originally submitted model file for PLaSMo accession ID PLM_75, version 1

Creators: BioData SynthSys, Yin Hoon Chew

Submitter: BioData SynthSys

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

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

Creators: Dawie van Niekerk, Jacky Snoep

Submitter: Dawie van Niekerk

PGK model for S. solfataricus

Creator: Jacky Snoep

Submitter: Jacky Snoep

PGK 70C SBML

Creator: Jacky Snoep

Submitter: Jacky Snoep

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

Creator: Jacky Snoep

Submitter: Jacky Snoep

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

PGK yeast Fig1a

Creator: Jacky Snoep

Submitter: Jacky Snoep

PGK yeast with/without recycling

Creator: Jacky Snoep

Submitter: Jacky Snoep

PGK-GAPDH model Sulfolobus kouril8

Creator: Jacky Snoep

Submitter: Jacky Snoep

PGK-GAPDH model yeast kouril7

Creator: Jacky Snoep

Submitter: Jacky Snoep

PGK-GAPDH models yeast and Sulfolobus Fig. 4 in manuscript

Creator: Jacky Snoep

Submitter: Jacky Snoep

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

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

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

No description specified

Creator: Paul Heusden

Submitter: The JERM Harvester

Model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG, with sequential addition of purified enzymes.

Creator: Jacky Snoep

Submitter: Jacky Snoep

Model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG upon sequential adition of purified enzymes. If the Mathematica notebook is downloaded and the data file is downloaded in the same directory, then the notebook can be evaluated, and the figure in the manuscript for the progress curves will be reproduced.

Creator: Jacky Snoep

Submitter: Jacky Snoep

Model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG upon sequential adition of purified enzymes. If the Mathematica notebook is downloaded and the data file is downloaded in the same directory, then the notebook can be evaluated, and the figure in the manuscript for the progress curves will be reproduced.

Creator: Jacky Snoep

Submitter: Jacky Snoep

Model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG upon sequential adition of purified enzymes. If the Mathematica notebook is downloaded and the data file is downloaded in the same directory, then the notebook can be evaluated, and the figure in the manuscript for the progress curves will be reproduced.

Creator: Jacky Snoep

Submitter: Jacky Snoep

Model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG upon sequential adition of purified enzymes. If the Mathematica notebook is downloaded and the data file is downloaded in the same directory, then the notebook can be evaluated, and the figure in the manuscript for the progress curves will be reproduced.

Creator: Jacky Snoep

Submitter: Jacky Snoep

Model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG upon sequential adition of purified enzymes. If the Mathematica notebook is downloaded and the data file is downloaded in the same directory, then the notebook can be evaluated, and the figure in the manuscript for the progress curves will be reproduced.

Creator: Jacky Snoep

Submitter: Jacky Snoep

Model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG upon sequential adition of purified enzymes. If the Mathematica notebook is downloaded and the data file is downloaded in the same directory, then the notebook can be evaluated, and the figure in the manuscript for the progress curves will be reproduced.

Creator: Jacky Snoep

Submitter: Jacky Snoep

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

Creators: Jennifer Levering, Mark Musters

Submitter: Jennifer Levering

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

Creator: Jennifer Levering

Submitter: 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

Submitter: Nadine Veith

Pyrimidine deprivation and immune response related to human coronavirus infection

Creators: Zsolt Bocskei, Franck Augé, Anna Niarakis

Submitter: Marek Ostaszewski

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

Creators: Dawie van Niekerk, Jacky Snoep

Submitter: Dawie van Niekerk

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