Drug-target Binding Affinity Prediction Based on Three-branched Multiscale Convolutional Neural Networks

Background: New drugs are costly, time-consuming, and often accompanied by safety concerns. With the development of deep learning, computer-aided drug design has become more mainstream, and convolutional neural networks and graph neural networks have been widely used for drug–target affinity (DTA) prediction. Objective: The paper proposes a method of predicting DTA using graph convolutional networks and multiscale convolutional neural networks. Methods: We construct drug molecules into graph representation vectors and learn feature expressions through graph attention networks and graph convolutional networks. A three-branch convolutional neural network learns the local and global features of protein sequences, and the two feature representations are merged into a regression module to predict the DTA. Results: We present a novel model to predict DTA, with a 2.5% improvement in the consistency index and a 21% accuracy improvement in terms of the mean squared error on the Davis dataset compared to DeepDTA. Morever, our method outperformed other mainstream DTA prediction models namely, GANsDTA, WideDTA, GraphDTA and DeepAffinity. Conclusion: The results showed that the use of multiscale convolutional neural networks was better than a single-branched convolutional neural network at capturing protein signatures and the use of graphs to express drug molecules yielded better results.