Assays

20 Assays visible to you, out of a total of 20

Computational pathway design for biotechnological applications

PPK kinetic data for initial rate experiments and for enzyme incubations are linked and available in an Excel file. In addition a model file is available as Mathematica notebook for the parameterization of a rate equation for the enzyme, and for simulation of the enzyme incubations.

Submitter: Jacky Snoep

Assay type: Experimental Assay Type

Technology type: Initial Rate Experiment

Investigation: Polyphosphate kinases in Sulfolobus acidocaldarius

Study: PPK kinetics and incubations

Organisms: No organisms

SOPs: No SOPs

Data files: Experimental data file PPK kinetics, model file PPK incubations, model file for PPK kinetics

Snapshots: No snapshots

Created: 30th Jan 2026 at 13:52, Last updated: 30th Jan 2026 at 14:07

Cell free extract, without added Mn, with NAD recycling

Computational pathway design for biotechnological applications

Conversion of XYL to KG in a cell free extract of Caulobacter crescentus, without Mn2+ added, but with NAD recycling, metabolites measured enzymatically. https://jjj.bio.vu.nl/models/experiments/shen2020_fig4d/simulate

Submitter: Jacky Snoep

Biological problem addressed: Model Analysis Type

Investigation: Caulobacter crescentus Weimberg pathway

Study: Cell free extract

Organisms: No organisms

Models: CFE analysis (shen2), CFE no Mn, with NADrec

SOPs: No SOPs

Data files: CFE no-Mn but with NADrec data

Snapshots: Snapshot 1, Snapshot 2

DOI: 10.15490/fairdomhub.1.assay.995.2

Created: 11th Apr 2019 at 09:18, Last updated: 8th Jan 2020 at 15:12

Cell free extract, with Mn, no NAD recycling

Computational pathway design for biotechnological applications

Conversion of XYL to KG in a cell free extract of Caulobacter crescentus, with 0.15 mM Mn2+ added, but no NAD recycling, metabolites measured enzymatically. https://jjj.bio.vu.nl/models/experiments/shen2020_fig4c/simulate

Submitter: Jacky Snoep

Biological problem addressed: Model Analysis Type

Investigation: Caulobacter crescentus Weimberg pathway

Study: Cell free extract

Organisms: No organisms

Models: CFE Mn noNADrec, CFE analysis (shen2)

SOPs: No SOPs

Data files: CFE Mn no-NADrec data

Snapshots: Snapshot 1, Snapshot 2

DOI: 10.15490/fairdomhub.1.assay.994.2

Created: 11th Apr 2019 at 09:16, Last updated: 8th Jan 2020 at 15:11

Cell free extract, with Mn and NAD recycling

Computational pathway design for biotechnological applications

Conversion of XYL to KG in a cell free extract of Caulobacter crescentus, with 0.15 mM Mn2+ added, and with NAD recycling, metabolites measured enzymatically. https://jjj.bio.vu.nl/models/experiments/shen2020_fig4b/simulate

Submitter: Jacky Snoep

Biological problem addressed: Model Analysis Type

Investigation: Caulobacter crescentus Weimberg pathway

Study: Cell free extract

Organisms: No organisms

Models: CFE Mn NADrec, CFE analysis (shen2)

SOPs: No SOPs

Data files: CFE Mn NADrec data

Snapshots: Snapshot 1, Snapshot 2

DOI: 10.15490/fairdomhub.1.assay.993.2

Created: 11th Apr 2019 at 08:15, Last updated: 8th Jan 2020 at 15:10

One pot cascade 16

Computational pathway design for biotechnological applications

Conversion of XYL to KG in one pot cascade of Weimberg pathway enzymes of Caulobacter crescentus, using old enzymes with optimal protein distribution, with NAD recycling, measured in NMR. https://jjj.bio.vu.nl/models/experiments/shen2020_fig3d/simulate

Submitter: Jacky Snoep

Biological problem addressed: Model Analysis Type

Investigation: Caulobacter crescentus Weimberg pathway

Study: One pot cascade

Organisms: No organisms

Models: Cascade analysis (shen2), One pot cascade 16

SOPs: No SOPs

Data files: One-Pot-Cascade 16 data

Snapshots: Snapshot 1, Snapshot 2

DOI: 10.15490/fairdomhub.1.assay.991.2

Created: 10th Apr 2019 at 09:59, Last updated: 8th Jan 2020 at 15:10

One pot cascade 13

Computational pathway design for biotechnological applications

Conversion of XYL to KG in one pot cascade of Weimberg pathway enzymes of Caulobacter crescentus, with NAD recycling, measured in NMR. https://jjj.bio.vu.nl/models/experiments/shen2020_fig3b/simulate

Submitter: Jacky Snoep

Biological problem addressed: Model Analysis Type

Investigation: Caulobacter crescentus Weimberg pathway

Study: One pot cascade

Organisms: No organisms

Models: Cascade analysis (shen2), One-Pot-Cascade 13

SOPs: No SOPs

Data files: One-Pot-Cascade 13 data

Snapshots: Snapshot 1, Snapshot 2

DOI: 10.15490/fairdomhub.1.assay.989.2

Created: 9th Apr 2019 at 14:05, Last updated: 8th Jan 2020 at 15:09

One pot cascade 12

Computational pathway design for biotechnological applications

Conversion of XYL to KG in one pot cascade of Weimberg pathway enzymes of Caulobacter crescentus, omitting XLA, measured in NMR. https://jjj.bio.vu.nl/models/experiments/shen2020_fig3c/simulate

Submitter: Jacky Snoep

Biological problem addressed: Model Analysis Type

Investigation: Caulobacter crescentus Weimberg pathway

Study: One pot cascade

Organisms: No organisms

Models: Cascade analysis (shen2), One pot cascade 12

SOPs: No SOPs

Data files: One-Pot-Cascade 12 data

Snapshots: Snapshot 1, Snapshot 2

DOI: 10.15490/fairdomhub.1.assay.988.2

Created: 9th Apr 2019 at 14:05, Last updated: 8th Jan 2020 at 15:09

One pot cascade 10

Computational pathway design for biotechnological applications

Conversion of XYL to KG in one pot cascade of Weimberg pathway enzymes of Caulobacter crescentus, measured in NMR. https://jjj.bio.vu.nl/models/experiments/shen2020_fig3a/simulate

Submitter: Jacky Snoep

Biological problem addressed: Model Analysis Type

Investigation: Caulobacter crescentus Weimberg pathway

Study: One pot cascade

Organisms: No organisms

Models: Cascade analysis (shen2), One-Pot-Cascade 10

SOPs: No SOPs

Data files: One-Pot-Cascade 10 data

Snapshots: Snapshot 1, Snapshot 2

DOI: 10.15490/fairdomhub.1.assay.987.2

Created: 9th Apr 2019 at 14:02, Last updated: 8th Jan 2020 at 15:09

Progress curves combined

Computational pathway design for biotechnological applications

Conversion of XYL to KG by sequential addition of Weimberg pathway enzymes of Caulobacter crescentus, measured in NMR. https://jjj.bio.vu.nl/models/experiments/shen2020_fig2c/simulate

Submitter: Jacky Snoep

Biological problem addressed: Model Analysis Type

Investigation: Caulobacter crescentus Weimberg pathway

Study: Progress curves

Organisms: No organisms

Models: Progress curve analysis (shen1), Progress curve analysis combined

SOPs: No SOPs

Data files: Progress curve analysis data

Snapshots: Snapshot 1, Snapshot 2

DOI: 10.15490/fairdomhub.1.assay.986.2

Created: 9th Apr 2019 at 12:25, Last updated: 8th Jan 2020 at 15:08

Steady state cell free extract, with Mn and NAD recycling

Computational pathway design for biotechnological applications

No description specified

Submitter: Jacky Snoep

Biological problem addressed: Model Analysis Type

Investigation: Caulobacter crescentus Weimberg pathway

Study: Cell free extract

Organisms: No organisms

Models: CFE steady state analysis (shen3)

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 29th Nov 2019 at 16:49, Last updated: 6th Jan 2020 at 15:17

XDH

Computational pathway design for biotechnological applications

Kinetic characterisation and mathematical modelling of XDH.

Submitter: Jacky Snoep

Biological problem addressed: Model Analysis Type

Investigation: Caulobacter crescentus Weimberg pathway

Study: Initial rate kinetics

Organisms: No organisms

Models: XDH model

SOPs: No SOPs

Data files: XDH-initial rate kinetics data

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.968.1

Created: 26th Mar 2019 at 14:37, Last updated: 6th Jan 2020 at 15:17

XLA

Computational pathway design for biotechnological applications

Kinetic characterisation and mathematical modelling of XLA.

Submitter: Jacky Snoep

Biological problem addressed: Model Analysis Type

Investigation: Caulobacter crescentus Weimberg pathway

Study: Initial rate kinetics

Organisms: No organisms

Models: XLA model

SOPs: No SOPs

Data files: XLA-initial rate kinetics data

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.969.1

Created: 26th Mar 2019 at 14:41, Last updated: 6th Jan 2020 at 15:17

XAD

Computational pathway design for biotechnological applications

Kinetic characterisation and mathematical modelling of XAD.

Submitter: Jacky Snoep

Biological problem addressed: Model Analysis Type

Investigation: Caulobacter crescentus Weimberg pathway

Study: Initial rate kinetics

Organisms: No organisms

Models: XAD model

SOPs: No SOPs

Data files: XAD-initial rate kinetics data

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.970.1

Created: 26th Mar 2019 at 14:41, Last updated: 6th Jan 2020 at 15:17

KDXD

Computational pathway design for biotechnological applications

Kinetic characterisation and mathematical modelling of KDXD.

Submitter: Jacky Snoep

Biological problem addressed: Model Analysis Type

Investigation: Caulobacter crescentus Weimberg pathway

Study: Initial rate kinetics

Organisms: No organisms

Models: KDXD model

SOPs: No SOPs

Data files: KDXD-initial rate kinetics data

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.971.1

Created: 26th Mar 2019 at 14:42, Last updated: 6th Jan 2020 at 15:17

KGSADH

Computational pathway design for biotechnological applications

Kinetic characterisation and mathematical modelling of KGSADH.

Submitter: Jacky Snoep

Biological problem addressed: Model Analysis Type

Investigation: Caulobacter crescentus Weimberg pathway

Study: Initial rate kinetics

Organisms: No organisms

Models: KGSADH model

SOPs: No SOPs

Data files: KGSADH-initial rate kinetics data

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.972.1

Created: 26th Mar 2019 at 14:42, Last updated: 6th Jan 2020 at 15:17

Progress curve XDH

Computational pathway design for biotechnological applications

Conversion of Xyl to XLAC by Caulobacter crescentus XDH, measured in NMR.

Submitter: Jacky Snoep

Biological problem addressed: Model Analysis Type

Investigation: Caulobacter crescentus Weimberg pathway

Study: Progress curves

Organisms: No organisms

Models: Progress curve analysis (shen1), Progress curve analysis XDH

SOPs: No SOPs

Data files: Progress curve analysis data

Snapshots: Snapshot 1, Snapshot 2

DOI: 10.15490/fairdomhub.1.assay.978.2

Created: 30th Mar 2019 at 11:34, Last updated: 6th Jan 2020 at 15:17

Progress curve XLA

Computational pathway design for biotechnological applications

Conversion of XLAC to XA by Caulobacter crescentus XLA, measured in NMR.

Submitter: Jacky Snoep

Biological problem addressed: Model Analysis Type

Investigation: Caulobacter crescentus Weimberg pathway

Study: Progress curves

Organisms: No organisms

Models: Progress curve analysis (shen1), Progress curve analysis XLA

SOPs: No SOPs

Data files: Progress curve analysis data

Snapshots: Snapshot 1, Snapshot 2

DOI: 10.15490/fairdomhub.1.assay.979.2

Created: 30th Mar 2019 at 18:41, Last updated: 6th Jan 2020 at 15:17

Progress curve XAD

Computational pathway design for biotechnological applications

Conversion of XA to KDX by Caulobacter crescentus XAD, measured in NMR.

Submitter: Jacky Snoep

Biological problem addressed: Model Analysis Type

Investigation: Caulobacter crescentus Weimberg pathway

Study: Progress curves

Organisms: No organisms

Models: Progress curve analysis (shen1), Progress curve analysis XAD

SOPs: No SOPs

Data files: Progress curve analysis data

Snapshots: Snapshot 1, Snapshot 2

DOI: 10.15490/fairdomhub.1.assay.980.2

Created: 30th Mar 2019 at 18:42, Last updated: 6th Jan 2020 at 15:17

Progress curve KDXD

Computational pathway design for biotechnological applications

Conversion of KDX to KGSA by Caulobacter crescentus KDXD, measured in NMR.

Submitter: Jacky Snoep

Biological problem addressed: Model Analysis Type

Investigation: Caulobacter crescentus Weimberg pathway

Study: Progress curves

Organisms: No organisms

Models: Progress curve analysis (shen1), Progress curve analysis KDXD

SOPs: No SOPs

Data files: Progress curve analysis data

Snapshots: Snapshot 1, Snapshot 2

DOI: 10.15490/fairdomhub.1.assay.981.2

Created: 30th Mar 2019 at 18:43, Last updated: 6th Jan 2020 at 15:17

Progress curve KGSADH

Computational pathway design for biotechnological applications

Conversion of KGSA to KG by Caulobacter crescentus KGSADH, measured in NMR.

Submitter: Jacky Snoep

Biological problem addressed: Model Analysis Type

Investigation: Caulobacter crescentus Weimberg pathway

Study: Progress curves

Organisms: No organisms

Models: Progress curve analysis (shen1), Progress curve analysis KGSADH

SOPs: No SOPs

Data files: Progress curve analysis data

Snapshots: Snapshot 1, Snapshot 2

DOI: 10.15490/fairdomhub.1.assay.982.2

Created: 30th Mar 2019 at 18:44, Last updated: 6th Jan 2020 at 15:17

Assays

Filters ×

Filters