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InteractionGNN

Source code to run InteractionGNN on protein-protein interfaces

Usage

  1. Set the desired parameters in config.ini
  2. in a bash shell, run python interaction_gnn.py

Requirements

Packages:
  • Manual: install Pytorch, Pytorch-Geometric, Cuda-Toolkit, Scikit-Learn and the packages numpy pandas matplotlib lz4 and tqdm (conda install -c pytorch -c pyg -c conda-forge python=3.9 numpy pandas matplotlib tqdm pytorch pyg scikit-learn cuda-toolkit lz4)
  • All-in-one: Run conda create --name interaction_gnn --file interaction_gnn.yml
    InteractionGNN is using Pytorch-Geometric.
Data files:

Should be in the folder data, displayed like the following example for binary classification: \

InteractionGNN
|   interaction_gnn.py
|
|___src
|   |   ...
|
|___data
    |___protein_pair_1
    |   |___0
    |   |   |   file1
    |   |   |   file2
    |   |
    |   |___1
    |       |   file3
    |       |   file4
    |   
    |___protein_pair_2
    |   |___0
    |   |   |   file5
    |   |   |   file6
    |   |
    |   |___1
    |       |   file7
    |       |   file8
    ..........

Citing

If you use this code, please cite the associated paper:
Y. Mohseni Behbahani, S. Crouzet, E. Laine, A. Carbone, *Deep Local Analysis evaluates protein docking conformations with locally oriented cubes*