DeepDR: an integrated deep-learning model web server for drug repositioning

TL;DR

DeepDR is an integrated deep-learning web platform that combines multiple models and a vast knowledge graph to facilitate drug repositioning with high accuracy and interpretability.

Contribution

This paper introduces DeepDR, the first platform integrating diverse DL models and a large knowledge graph for disease- and target-specific drug repositioning.

Findings

Supports over 15 networks and 5.9 million edges in the knowledge graph

Provides detailed drug descriptions and visualization of key patterns

Accessible without registration, promoting widespread use

Abstract

Background: Identifying new indications for approved drugs is a complex and time-consuming process that requires extensive knowledge of pharmacology, clinical data, and advanced computational methods. Recently, deep learning (DL) methods have shown their capability for the accurate prediction of drug repositioning. However, implementing DL-based modeling requires in-depth domain knowledge and proficient programming skills. Results: In this application, we introduce DeepDR, the first integrated platform that combines a variety of established DL-based models for disease- and target-specific drug repositioning tasks. DeepDR leverages invaluable experience to recommend candidate drugs, which covers more than 15 networks and a comprehensive knowledge graph that includes 5.9 million edges across 107 types of relationships connecting drugs, diseases, proteins/genes, pathways, and expression from six existing databases and a large scientific corpus of 24 million PubMed publications. Additionally, the recommended results include detailed descriptions of the recommended drugs and visualize key patterns with interpretability through a knowledge graph. Conclusion: DeepDR is free and open to all users without the requirement of registration. We believe it can provide an easy-to-use, systematic, highly accurate, and computationally automated platform for both experimental and computational scientists.