A Multibranch Neural Network for Drug-Target Affinity Prediction Using Similarity Information.

Abstract

Predicting drug-target affinity (DTA) is beneficial for accelerating drug discovery. In recent years, graph structure-based deep learning models have garnered significant attention in this field. However, these models typically handle drug or target protein in isolation and only extract the molecular structure information on the drug or protein itself. To address this limitation, existing network-based models represent drug-target interactions or affinities as a knowledge graph to capture the interaction information. In this study, we propose a novel solution. Specifically, we introduce drug similarity information and protein similarity information into the field of DTA prediction. Moreover, we propose a network framework that autonomously extracts similarity information, avoiding reliance on knowledge graphs. Based on this framework, we design a multibranch neural network called GASI-DTA. This network integrates similarity information, sequence information, and molecular structure information. Comprehensive experimental results conducted on two benchmark data sets and three cold-start scenarios demonstrate that our model outperforms state-of-the-art graph structure-based methods in nearly all metrics. Furthermore, it exhibits significant advantages over existing network-based models, outperforming the best of them in the majority of metrics. Our study's code and data are openly accessible at http://github.com/XiaoLin-Yang-S/GASI-DTA.