Prediction of Drug-Target Interactions Using Molecular Graph and GDNet-DTI Model
Shuai Xu, Xiaoli Lin, Haiping Yu · 2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) · 2021
The prediction of drug-target interactions (DTIs) is of great significance to the fields of drug design and drug development. However, traditional biological experiments are time-consuming and cost-effective, which has prompted more people to turn their attention to the use of computers to assist in predicting DTIs. This paper proposes an improved prediction model based on multiple graph representation methods, which is GDNet-DTI that combined GCN and DeepWalk. First, a molecular map with atoms as nodes and chemical bonds as edges is generated using the SMILE sequence of drugs, and then GIN is used to extract the features of molecular map for better obtaining the complex interactions between atoms. For target proteins, the protein sequence is first represented by a word vector, and then the one-dimensional convolution is used to extract features for extracting the different levels of features. Then, based on obtained drug features and target features, a DTI-graph is generated, in which drugs and targets are represented as nodes and interactions are represented as edges. Finally, GDNet-DTI are used to obtain node neighborhood information and graph topology information of the DTI-graph. Compared with other advanced models, the results show that GDNet-DTI combined with multiple graph features can predict DTIs more accurately and effectively with DrugBank and four benchmark datasets. In addition, a case study with COVID-19 data is presented, which shows that the proposed method has the potential to predict the actual DTIs and can contribute to the development of drug discovery.