Identifying drug–target interactions based on graph convolutional network and deep neural network

• Published in: Briefings in bioinformatics Vol. 22; no. 2; pp. 2141 - 2150
• Main Authors: Zhao, Tianyi, Hu, Yang, Valsdottir, Linda R, Zang, Tianyi, Peng, Jiajie
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 22.03.2021; Oxford Publishing Limited (England)
• Subjects: Artificial neural networks; Computer applications; Drugs; Graph theory; Machine learning; Neural networks; Proteins; Target recognition; Therapeutic targets; graph convolutional network; drug–target interaction prediction; deep neural network; biological networks
• DOI: 10.1093/bib/bbaa044
• ISSN: 1467-5463; 1477-4054

Abstract Identification of new drug–target interactions (DTIs) is an important but a time-consuming and costly step in drug discovery. In recent years, to mitigate these drawbacks, researchers have sought to identify DTIs using computational approaches. However, most existing methods construct drug networks and target networks separately, and then predict novel DTIs based on known associations between the drugs and targets without accounting for associations between drug–protein pairs (DPPs). To incorporate the associations between DPPs into DTI modeling, we built a DPP network based on multiple drugs and proteins in which DPPs are the nodes and the associations between DPPs are the edges of the network. We then propose a novel learning-based framework, ‘graph convolutional network (GCN)-DTI’, for DTI identification. The model first uses a graph convolutional network to learn the features for each DPP. Second, using the feature representation as an input, it uses a deep neural network to predict the final label. The results of our analysis show that the proposed framework outperforms some state-of-the-art approaches by a large margin.