Machine Learning for Drug-Target Interaction Prediction.
Chen Ruolan,Liu Xiangrong,Jin Shuting,Lin Jiawei,Liu Juan
Molecules (Basel, Switzerland)
Identifying drug-target interactions will greatly narrow down the scope of search of candidate medications, and thus can serve as the vital first step in drug discovery. Considering that in vitro experiments are extremely costly and time-consuming, high efficiency computational prediction methods could serve as promising strategies for drug-target interaction (DTI) prediction. In this review, our goal is to focus on machine learning approaches and provide a comprehensive overview. First, we summarize a brief list of databases frequently used in drug discovery. Next, we adopt a hierarchical classification scheme and introduce several representative methods of each category, especially the recent state-of-the-art methods. In addition, we compare the advantages and limitations of methods in each category. Lastly, we discuss the remaining challenges and future outlook of machine learning in DTI prediction. This article may provide a reference and tutorial insights on machine learning-based DTI prediction for future researchers.
Drug-target interaction prediction: databases, web servers and computational models.
Chen Xing,Yan Chenggang Clarence,Zhang Xiaotian,Zhang Xu,Dai Feng,Yin Jian,Zhang Yongdong
Briefings in bioinformatics
Identification of drug-target interactions is an important process in drug discovery. Although high-throughput screening and other biological assays are becoming available, experimental methods for drug-target interaction identification remain to be extremely costly, time-consuming and challenging even nowadays. Therefore, various computational models have been developed to predict potential drug-target associations on a large scale. In this review, databases and web servers involved in drug-target identification and drug discovery are summarized. In addition, we mainly introduced some state-of-the-art computational models for drug-target interactions prediction, including network-based method, machine learning-based method and so on. Specially, for the machine learning-based method, much attention was paid to supervised and semi-supervised models, which have essential difference in the adoption of negative samples. Although significant improvements for drug-target interaction prediction have been obtained by many effective computational models, both network-based and machine learning-based methods have their disadvantages, respectively. Furthermore, we discuss the future directions of the network-based drug discovery and network approach for personalized drug discovery based on personalized medicine, genome sequencing, tumor clone-based network and cancer hallmark-based network. Finally, we discussed the new evaluation validation framework and the formulation of drug-target interactions prediction problem by more realistic regression formulation based on quantitative bioactivity data.
Computational Model Development of Drug-Target Interaction Prediction: A Review.
Zhao Qi,Yu Haifan,Ji Mingxuan,Zhao Yan,Chen Xing
Current protein & peptide science
In the medical field, drug-target interactions are very important for the diagnosis and treatment of diseases, they also can help researchers predict the link between biomolecules in the biological field, such as drug-protein and protein-target correlations. Therefore, the drug-target research is a very popular study in both the biological and medical fields. However, due to the limitations of manual experiments in the laboratory, computational prediction methods for drug-target relationships are increasingly favored by researchers. In this review, we summarize several computational prediction models of the drug-target connections during the past two years, and briefly introduce their advantages and shortcomings. Finally, several further interesting research directions of drug-target interactions are listed.