PPIOD: protein interface prediction through outlier detection

CnnDTI: Predicting drug-target interactions from drug structure and protein sequence

using novel convolutional neural networks

Abstract:

Background: Accurate identification of potential interactions between drugs and protein targets is a critical step to accelerate drug discovery. Despite many relative experimental researches have been done in the past decades, detecting drug-target interactions (DTIs) remains to be extremely resource-intensive and time-consuming. Therefore, many computational approaches have been developed for predicting drug-target associations on a large scale.

Results: In this paper, we proposed an deep learning-based method to predict DTIs only using the information of drug structures and protein sequences. The final results showed that our method can achieve good performance with the accuracies up to 92.0%, 90.0%, 92.0% and 90.7% for the target families of enzymes, ion channels, GPCRs and nuclear receptors of our created dataset, respectively. Another dataset derived from DrugBank was used to further assess the generalization of the model, which yielded an accuracy of 0.9015 and an AUC value of 0.9557.

Conclusion: It was elucidated that our model shows improved performance in comparison with other state-of-the-art computational methods on the common benchmark datasets. Experimental results demonstrated that our model successfully extracted more nuanced yet useful features, and therefore can be used as a practical tool to discover new drugs.

Supplementary files:

Additional file 1: This file records the detailed drug-target pairs on enzymes, ion channels, GPCRs and nuclear receptors of the Dataset2.

Additional file 2: In this file, to obtain the optimal learning rate of our model, a series of different learning rates are explored on each types of protein families of both Dataset1 and Dataset2.

Citation:

ShanShan Hu, Chenglin Zhang, Peng Chen, Pengying Gu, Jun Zhang and Bing Wang, Predicting drug-target interactions from drug structure and protein sequence using novel convolutional neural networks, BMC Bioinformatics.