PLA-Net: Predicting Protein-Ligand Interactions with Deep Graph Networks

Forked version of PLA-Net

Original paper on Nature Scientific Reports

Background

PLA-Net is a deep learning model designed to predict interactions between small organic molecules (ligands) and any of the 102 target proteins in the Alzheimer's Disease (AD) dataset. By transforming molecular and protein sequences into graph representations, PLA-Net leverages Graph Convolutional Networks (GCNs) to analyze and predict target-ligand interaction probabilities. Developed by BCV-Uniandes.

Quick Start

If you want to run PLA-Net without installing it, you can run it freely on this Hugging Face Space.

You can also use the provided notebook in the notebooks folder to run inference on the PLA-Net model with the gradio client.

Key Features

• Graph-Based Input Representation

  • Ligand Module (LM): Converts SMILES sequences of molecules into graph representations.
  • Protein Module (PM): Transforms FASTA sequences of proteins into graph structures.

• Deep Graph Convolutional Networks

  • Each module employs a deep GCN followed by an average pooling layer to extract meaningful features from the input graphs.

• Interaction Prediction

  • The feature representations from the LM and PM are concatenated.
  • A fully connected layer processes the combined features to predict the interaction probability between the ligand and the target protein.

Docker Install

To prevent conflicts with the host machine, it is recommended to run PLA-Net in a Docker container.

First make sure you have an NVIDIA GPU and NVIDIA Container Toolkit installed. Then build the image with the following command:

docker build -t pla-net:latest .

Inference

To run inference, run the following command:

docker run \
    -it --rm --gpus all \
    -v "$(pwd)":/home/user/output \
    pla-net:latest \
    python /home/user/app/scripts/pla_net_inference.py \
    --use_gpu \
    --target ada \
    --target_list /home/user/app/data/datasets/AD/Targets_Fasta.csv \
    --target_checkpoint_path /home/user/app/example/checkpoints/BINARY_ada \
    --input_file_smiles /home/user/app/example/input_smiles.csv \
    --output_file /home/user/output/output_predictions.csv

This will run inference for the target protein ada with the SMILES in the input_smiles.csv file and save the predictions to the output_predictions.csv file.

The prediction file has the following format:

target,smiles,interaction_probability,interaction_class
ada,Cn4c(CCC(=O)Nc3ccc2ccn(CC[C@H](CO)n1cnc(C(N)=O)c1)c2c3)nc5ccccc45,0.9994347542524338,1

Where interaction_class is 1 if the interaction probability is greater than 0.5, and 0 otherwise.

Inference Args:

• use_gpu: Use GPU for inference.
• target: Target protein ID from the list of targets. Check the list of available targets in the data/targets.md file.
• target_list: Path to the target list CSV file.
• target_checkpoint_path: Path to the target checkpoint. (e.g. /workspace/pretrained-models/BINARY_ada) one checkpoint for each target.
• input_file_smiles: Path to the input SMILES file.
• output_file: Path to the output predictions file.

Gradio Server

We provide a simple graphical user interface to run PLA-Net with Gradio. To use it, run the following command:

docker run \
    -it --rm --gpus all \
    -p 7860:7860 \
    pla-net:latest \
    python app.py

Then open your browser and go to http://localhost:7860/ to access the web interface.

Local Install

To do inference with PLA-Net, you need to install the dependencies and activate the environment. You can use conda or mamba to install the dependencies. mamba is recommended because it is faster.

mamba env create -f environment.yml
mamba activate pla_net

Now you can run inference with PLA-Net locally. In the project folder, run the following command:

python scripts/pla_net_inference.py \
    --use_gpu \
    --target ada \
    --target_list data/datasets/AD/Targets_Fasta.csv \
    --target_checkpoint_path example/checkpoints/BINARY_ada \
    --input_file_smiles example/input_smiles.csv \
    --output_file example/output_predictions.csv

Jupyter Notebooks Experiments

The notebook PLA-Net-Local.ipynb contains the code to run inference and training experiments with PLA-Net.

In the project folder, run the following command if you are using a docker container:

docker run \
    -it --rm --gpus all \
    -p 8888:8888 \
    -v "$(pwd)":/home/user/app \
    pla-net:latest \
    jupyter lab --ip 0.0.0.0 --port 8888 

If you are not using a docker container, you can run the notebook directly in your local machine. While on the notebooks folder, run the following command:

jupyter lab --ip 0.0.0.0 --port 8888 

Go to http://0.0.0.0:8888/lab/tree/notebooks/PLA-Net-Local.ipynb, you will be prompted to enter a token, you can get the token from the terminal where the command was run.

Pre-trained Models Weights

You can download the pre-trained models from HuggingFace. The total size of all models is around 55GB.

git clone https://huggingface.co/juliocesar-io/PLA-Net

Whhen running inference update the --target_checkpoint_path parameter with your path, model name and target.

There are 4 models available:

• LM: Ligand Module trained on the AD dataset.
• LM+Advs: Ligand Module trained on the AD dataset with adversarial training.
• LMPM: Protein Module trained on the AD dataset using the weights of the Ligand Module.
• PLA-Net: Ligand Module + Protein Module + PLA-Net trained on the AD dataset.

Each of them has 102 targets models with 4 fold cross-validation. The folder structure is the following:

checkpoints/
    LM/
        BINARY_ada/
            Fold1/
                Best_Model.pth
            Fold2/
                Best_Model.pth
            ...
        ...
    LM+Advs/
        ...
    LMPM/
        ...
    PLA-Net/
        ...

Training

To do training, refer to the train.sh script. There you can set the models to train, the targets and other parameters. Use the TARGET variable to set the target protein and EXPERIMENT to set the experiment name. Review the parameters and run the script.

To start training, run the following command:

bash train.sh

Then you can run evaluation for each of the models with the scripts in the evaluation folder. For example, to run evaluation for the PLA-Net model, you can run the following command:

bash evaluation/PLA-Net.sh

Citation

Ruiz Puentes, P., Rueda-Gensini, L., Valderrama, N. et al. Predicting target–ligand interactions with graph convolutional networks for interpretable pharmaceutical discovery. Sci Rep 12, 8434 (2022). https://doi.org/10.1038/s41598-022-12180-x