PINDeL

Protein Interaction Network-based Deep Learning Framework for Identifying Disease-Associated Human Proteins

Please download and unzip 'Executable.zip'.

The extracted folder 'Executable' consists of the following files:

Input:

1. hplg.features --> File storing the topological features' measures for all the nodes/proteins of the HPLG.
2. label.pkl --> File storing the labels (Control/Disease) corresponding to each protein.
3. network_wcc.pkl --> File storing the HPLG network.
4. nodes.pkl --> File containing the list of proteins present in the HPLG.
5. pindel.pt --> Our trained model.
6. pbd.yml --> Conda environment file.
7. pbd.py --> Source code.

Requirements:

1. Anaconda

Create environment:

For execution, we recommend to create a separate environment in Anaconda. The image of the required environment (pbd.yml) is given in this package. First create the environment and activate it by executing the following commands,

conda env create -f pbd.yml

conda activate pbd

Run:

Run the pbd.py file.

For any doubts or suggestions please contact [email protected]