title: Network predicting drug's anatomical therapeutic chemical code.
abstract: BACKGROUND
  Discovering drug's Anatomical Therapeutic Chemical (ATC) classification rules at molecular level is of vital importance to understand a vast majority of drugs action. However, few studies attempt to annotate drug's potential ATC-codes by computational approaches.
  
  
  RESULTS
  Here, we introduce drug-target network to computationally predict drug's ATC-codes and propose a novel method named NetPredATC. Starting from the assumption that drugs with similar chemical structures or target proteins share common ATC-codes, our method, NetPredATC, aims to assign drug's potential ATC-codes by integrating chemical structures and target proteins. Specifically, we first construct a gold-standard positive dataset from drugs' ATC-code annotation databases. Then we characterize ATC-code and drug by their similarity profiles and define kernel function to correlate them. Finally, we use a kernel method, support vector machine, to automatically predict drug's ATC-codes. Our method was validated on four drug datasets with various target proteins, including enzymes, ion channels, G-protein couple receptors and nuclear receptors. We found that both drug's chemical structure and target protein are predictive, and target protein information has better accuracy. Further integrating these two data sources revealed more experimentally validated ATC-codes for drugs. We extensively compared our NetPredATC with SuperPred, which is a chemical similarity-only based method. Experimental results showed that our NetPredATC outperforms SuperPred not only in predictive coverage but also in accuracy. In addition, database search and functional annotation analysis support that our novel predictions are worthy of future experimental validation.
  
  
  CONCLUSIONS
  In conclusion, our new method, NetPredATC, can predict drug's ATC-codes more accurately by incorporating drug-target network and integrating data, which will promote drug mechanism understanding and drug repositioning and discovery.
  
  
  BACKGROUND
  NetPredATC is available at http://doc.aporc.org/wiki/NetPredATC.
  
  
  BACKGROUND
  ycwang@nwipb.cas.cn or ywang@amss.ac.cn
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810001, China.
authors.forename: Yong-Cui
authors.initials: YC
authors.lastname: Wang
authors.forename: Shi-Long
authors.initials: SL
authors.lastname: Chen
authors.forename: Nai-Yang
authors.initials: NY
authors.lastname: Deng
authors.forename: Yong
authors.initials: Y
authors.lastname: Wang
mesh_terms: D000465:Algorithms; D062313:Databases, Pharmaceutical; D016503:Drug Delivery Systems; D004364:Pharmaceutical Preparations / Q000737:chemistry*; D012984:Software
chemical_list: D004364:Pharmaceutical Preparations