IRAA: A statistical tool for investigating a protein-protein interaction interface from multiple structures

Jaydeep Belapure, Marija Sorokina, Panagiotis L. Kastritis

(https://doi.org/10.1002/pro.4523)

A GUI within ipynb

It is a tool to assess protein interface of a any complex [AB] with components [A] and [B]. Multiple 3D structures of complex [AB] in the bound state, as well as multiple 3D structrues of the components [A] and [B] are combined together to identify and understand the properties of the interface residues.

A Jupyter Notebook based GUI:

You can easily build the GUI within a jupyter notebook as shown below -

Github repos is structure as below:

Notebook -> Main file: jupyter notebook For a quick sneak peek the notebook file is converted to .html and .pdf format only for viewing purposes. To actually interact and run the analysis please open the Run_IRAA.ipynb and go through it cell-by-cell. At the beginning there is a simple GUI panel created within the notebook for easy interaction.

• iraa_utils -> contains scripts to offer some functionality ot the notebook
• figures -> all output figure will be saved here.
• data -> Contains downloaded mmCIF files data as well as processed SASA data.
• jpnb_overview_files -> Here are four .txt files, each containing lists of PDB IDs of structures of A, B, AB, and allow skipping any files a file _drop.txt.

Dependencies:

• numpy
• scipy
• pandas
• biopython
• tqdm
• pylab
• seaborn
• freesasa

You need to install freesasa and make sure it is added to the path, and available in your python run session.

Citation:

Please cite accordingly using (https://doi.org/10.1002/pro.4523) -

@article{belapure2023iraa,
  title={IRAA: A statistical tool for investigating a protein--protein interaction interface from multiple structures},
  author={Belapure, Jaydeep and Sorokina, Marija and Kastritis, Panagiotis L},
  journal={Protein Science},
  volume={32},
  number={1},
  pages={e4523},
  year={2023},
  publisher={Wiley Online Library}
}