Protein-protein interaction

Notebook to fit the model described in Roehrl et al, Biochemistry 43.51 (2004): 16056-16066 to experimental data.

Installation

We use conda to set up a specific Python environment containing all the packages we want to use.

1. Download this repository (either by using git clone https://github.com/nobias-fht/competitive_binding.git on the terminal or just downloading and unzipping).
2. If you don't have conda, install miniconda
3. In the command line terminal, navigate to the repository and type conda env create -f env.yml
4. Activate environment: conda activate protprot
5. Finally, start jupyter notebook by typing jupyter notebook and use the notebook.

Data format

The notebook expects the following format. for the .csv file:

L_T (uM)	C1 replicate 1 (%)	...	C2 replicate 1 (%)	...
0.01	56.23	...	...	...
0.1	...	...	...	...
10	...	...	...	...

The values should be separated by a comma (,) and the decimals indicated by a dot (.). Check out the example file.

⚠️ Make sure your data is in the proper format!