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Background  During the identification of potential candidates, computational prediction of drug-target interactions (DTIs) is important to subsequent expensive validation in wet-lab. DTI screening considers four scenarios, depending on whether the drug is an existing or a new drug and whether the target is an existing or a new target. However, existing approaches have the following limitations. First, only a few of them can address the most difficult scenario (i.e., predicting interactions between new drugs and new targets). More importantly, none of the existing approaches could provide the explicit information for understanding the mechanism of forming interactions, such as the drug-target feature pairs contributing to the interactions.    Results  In this paper, we propose a Triple Matrix Factorization-based model (TMF) to tackle these problems. Compared with former state-of-the-art predictive methods, TMF demonstrates its significant superiority by assessing the predictions on four benchmark datasets over four kinds of screening scenarios. Also, it exhibits its outperformance by validating predicted novel interactions. More importantly, by using PubChem fingerprints of chemical structures as drug features and occurring frequencies of amino acid trimer as protein features, TMF shows its ability to find out the features determining interactions, including dominant feature pairs, frequently occurring substructures, and conserved triplet of amino acids.    Conclusions  Our TMF provides a unified framework of DTI prediction for all the screening scenarios. It also presents a new insight for the underlying mechanism of DTIs by indicating dominant features, which play important roles in the forming of DTI.    Electronic supplementary material  The online version of this article (10.1186/s12918-018-0663-x) contains supplementary material, which is available to authorized users.

A unified solution for different scenarios of predicting drug-target interactions via triple matrix factorization