Volume 12, Number 07, April 2022

GDGRU-DTA: Predicting Drug-Target Binding Affinity based on GNN and Double GRU

  Authors

Lyu Zhijian, Jiang Shaohua, Liang Yigao and Gao Min, Hunan Normal University, China

  Abstract

The work for predicting drug and target affinity(DTA) is crucial for drug development and repurposing. In this work, we propose a novel method called GDGRU-DTA to predict the binding affinity between drugs and targets, which is based on GraphDTA, but we consider that protein sequences are long sequences, so simple CNN cannot capture the context dependencies in protein sequences well. Therefore, we improve it by interpreting the protein sequences as time series and extracting their features using Gate Recurrent Unit(GRU) and Bidirectional Gate Recurrent Unit(BiGRU). For the drug, our processing method is similar to that of GraphDTA, but uses two different graph convolution methods. Subsequently, the representation of drugs and proteins are concatenated for final prediction. We evaluate the proposed model on two benchmark datasets. Our model outperforms some state-of-the-art deep learning methods, and the results demonstrate the feasibility and excellent feature capture ability of our model.

  Keywords

Drug-Target Affinity, GRU, BiGRU, Graph Neural Network, Deep Learning.