SOPs

This is the Jupyter Notebook to allow editing and working with the code. It is a simple example of how a Selwyn test can look like if it is passed (1.) or failed (2.).

This is the pdf of the Jupyter Notebook to allow looking at the notebook without installing anything. It is a simple example of how a Selwyn test can look like if it is passed (1.) or failed (2.).

This is the Jupyter Notebook to allow editing and working with the code. It is a simple example of how a progress curve experiment can look like.

This is the pdf of the Jupyter Notebook to allow looking at the notebook without installing anything. It is a simple example of how a progress curve experiment can look like.

This is the pdf of the Jupyter Notebook to allow looking at the notebook without installing anything.

NOTE THAT this pdf may be mangled when viewed on FAIRDOMHub, but should look fine when downloaded.

This is a zip file containing all the files and folders needed to analyse raw data, fit initial rates and create a "Michaelis-Menten plot". Instructions on usage are added in the notebook.

This is the Jupyter Notebook to allow editing and working with the code.

Design an initial rate experiment in four steps

This script aims to help you design high-quality initial rate experiments. It uses the Michaelis-Menten equation to simulate data for an enzyme with unknown enzyme reaction parameters. Four steps are needed:

1. Estimate the enzyme reaction parameters

Input: estimates of Km and vmax

and indicate the enzyme concentration concentration you are planning to use. If you have no ...

This is the pdf of the Jupyter Notebook to allow looking at the notebook without installing anything.

Design an initial rate experiment in four steps

This script aims to help you design high-quality initial rate experiments. It uses the Michaelis-Menten equation to simulate data for an enzyme with unknown enzyme reaction parameters. Four steps are needed: 1. Estimate the enzyme reaction parameters

Input: estimates of Km and vmax

and indicate the enzyme concentration concentration you are planning ...

Gre2p activity monitored by NADPH absorbance using different enzyme concentrations. Activity is measured after different storage conditions (treatments) and in presence of different amounts of tween.

A python workflow is used to analyse the data and create a plot where the outcomes of the Selwyn test are plotted. It requires the following directory structure:

./Sewlyn_test_forS19.py ./tween/M1.csv ./tween/M2.csv ./tween/M3.csv ./tween/M4.csv ./treatments/M1.csv ./treatments/M2.csv ./treatments/M3.csv ...

Gre2p activity monitored by NADPH absorbance using different enzyme concentrations. Activity is measured after different storage conditions (treatments) and in presence of different amounts of tween. Also analysis of DLS data of homogeneity of Gre2p samples measured before and after these treatments.

A python workflow is used to analyse the data and create a plot of the data. It requires the following directory structure:

./Script_for_S13andS18.py ./Script_for_S22.py ./Script_for_S15.py

and as ...

SOP describing how to perform Dynamic Light Scattering (DLS) measurements with Gre2p in cuvettes using a Zetasizer Nano DLS reader.

SOP describing how to perform an ITC multiple injections experiment with a MicroCal PEAQ ITC by Malvern.

SOP describing how to perform an ITC (recurrent) single injections experiment with a MicroCal PEAQ ITC by Malvern.

Python workflow for the analysis of ITC-BIND, ITC-MIM and ITC-(r)SIM experiments. Organized in a *.zip folder. Requires the following directory structure:

./ITC_analysis.py ./input/BINDING/.apj ./input/BINDING/.csv ./input/KINETICS/.apj ./input/KINETICS/.csv ./scripts/binding_neu.py ./scripts/kinetics_neu.py

And can be executed by running python ITC_analysis.py in the directory. Filenames for the input *.apj and *.csv files are defined in ITC_analysis.py. The output directory is written by ...

SOP describing how to perform an ITC binding experiment with a MicroCal PEAQ ITC by Malvern. Note: the DOIs from the Chemotion database for the synthesis of HK and NDK are missing in this version beacuse the DOIs do not exist yet (as of 27.04.21)

SOP describing the steps for use of the ITC device (MicroCal PEAQ ITC by Malvern).

SOP describing how to perform specific activity measurements with Gre2p in multiwell plates (96w) using an UV-Vis Plate reader (Synergy H1).

SOP describing how to perform activity measurements (inital rates) with Gre2p in multiwell plates (96w) using an UV-Vis Plate reader (Synergy H1).

Instructions and details on the data analysis workflow.

Master Bash script to launch Molecular Dynamics when running the Simulation part of Simulation Foundry. Make sure you followed "Preparations" instructions! Read the Manual!

Master Bash script to launch Molecular Dynamics when running the Analysis part of Simulation Foundry. Make sure you followed "Preparations" instructions! Read the Manual!