title: Identification of chemogenomic features from drug-target interaction networks using interpretable classifiers.
abstract: BACKGROUND
  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 L(1) 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.
  
  
  BACKGROUND
  Softwares are available at the supplemental website.
  
  
  BACKGROUND
  yamanishi@bioreg.kyushu-u.ac.jp
  
  
  BACKGROUND
  Datasets and all results are available at http://cbio.ensmp.fr/~yyamanishi/l1binary/  .
authors.affiliation: ERATO Minato Project, Japan Science and Technology Agency, Sapporo 060-0814, Japan.
authors.forename: Yasuo
authors.initials: Y
authors.lastname: Tabei
authors.forename: Edouard
authors.initials: E
authors.lastname: Pauwels
authors.forename: Véronique
authors.initials: V
authors.lastname: Stoven
authors.forename: Kazuhiro
authors.initials: K
authors.lastname: Takemoto
authors.forename: Yoshihiro
authors.initials: Y
authors.lastname: Yamanishi
mesh_terms: D000465:Algorithms; D016503:Drug Delivery Systems; D015195:Drug Design; D006801:Humans; D008024:Ligands; D016014:Linear Models; D004364:Pharmaceutical Preparations / Q000737:chemistry*; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry / Q000145:classification / Q000378:metabolism
chemical_list: D008024:Ligands; D004364:Pharmaceutical Preparations; D011506:Proteins