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Alternatively, the computational methods provide a low-cost and high-efficiency way for predicting drug-target interactions (DTIs) from biomolecular networks. However, the current computational methods mainly deal with DTI predictions of known drugs; there are few methods for large-scale prediction of failed drugs and new chemical entities that are currently stored in some biological databases may be effective for other diseases compared with their originally targeted diseases. In this study, we propose a method (called SDTRLS) which predicts DTIs through RLS-Kron model with chemical substructure similarity fusion and Gaussian Interaction Profile (GIP) kernels. SDTRLS can be an effective predictor for targets of old drugs, failed drugs, and new chemical entities from large-scale biomolecular network databases. Our computational experiments show that SDTRLS outperforms the state-of-the-art SDTNBI method; specifically, in the G protein-coupled receptors (GPCRs) external validation, the maximum and the average AUC values of SDTRLS are 0.842 and 0.826, respectively, which are superior to those of SDTNBI, which are 0.797 and 0.766, respectively. This study provides an important basis for new drug development and drug repositioning based on biomolecular networks.<\/jats:p>","DOI":"10.1155\/2017\/2713280","type":"journal-article","created":{"date-parts":[[2017,12,3]],"date-time":"2017-12-03T18:30:58Z","timestamp":1512325858000},"page":"1-10","source":"Crossref","is-referenced-by-count":18,"title":["SDTRLS: Predicting Drug-Target Interactions for Complex Diseases Based on Chemical Substructures"],"prefix":"10.1155","volume":"2017","author":[{"given":"Cheng","family":"Yan","sequence":"first","affiliation":[{"name":"School of Information Science and Engineering, Central South University, Changsha, Hunan 410083, China"},{"name":"School of Computer and Information, Qiannan Normal University for Nationalities, Duyun, Guizhou 558000, 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