Identification of chemogenomic features from drug-target interaction networks using interpretable classifiers

Yasuo Tabei, Edouard Pauwels, Véronique Stoven, Kazuhiro Takemoto, Yoshihiro Yamanishi

Research output: Contribution to journalArticlepeer-review

74 Citations (Scopus)


Motivation: Drug effects are mainly caused by the interactions between drug molecules and their target proteins including primary targets and off-targets. Identification of the molecular mechanisms behind overall drug-target interactions is crucial in the drug design process. Results: We develop a classifier-based approach to identify chemogenomic features (the underlying associations between drug chemical substructures and protein domains) that are involved in drug-target interaction networks. We propose a novel algorithm for extracting informative chemogenomic features by using L1 regularized classifiers over the tensor product space of possible drug-target pairs. It is shown that the proposed method can extract a very limited number of chemogenomic features without loosing the performance of predicting drug-target interactions and the extracted features are biologically meaningful. The extracted substructure-domain association network enables us to suggest ligand chemical fragments specific for each protein domain and ligand core substructures important for a wide range of protein families.

Original languageEnglish
Article numberbts412
Pages (from-to)i487-i494
Issue number18
Publication statusPublished - Sept 2012

All Science Journal Classification (ASJC) codes

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics


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