Development of a graph convolutional neural network model for efficient prediction of protein-ligand binding affinities

Prediction of protein-ligand interactions is a critical step during the initial phase of drug discovery. We propose a novel deep-learning-based prediction model based on a graph convolutional neural network, named GraphBAR, for protein-ligand binding affinity. Graph convolutional neural networks reduce the computational time and resources that are normally required by the traditional convolutional neural network models. In this technique, the structure of a protein-ligand complex is represented as a graph of multiple adjacency matrices whose entries are affected by distances, and a feature matrix that describes the molecular properties of the atoms. We evaluated the predictive power of GraphBAR for protein-ligand binding affinities by using PDBbind datasets and proved the efficiency of the graph convolution. Given the computational efficiency of graph convolutional neural networks, we also performed data augmentation to improve the model performance. We found that data augmentation with docking simulation data could improve the prediction accuracy although the improvement seems not to be significant. The high prediction performance and speed of GraphBAR suggest that such networks can serve as valuable tools in drug discovery.