Genome-scale screening of drug-target associations relevant to Ki using a chemogenomics approach

PLoS One. 2013;8(4):e57680. doi: 10.1371/journal.pone.0057680. Epub 2013 Apr 5.


The identification of interactions between drugs and target proteins plays a key role in genomic drug discovery. In the present study, the quantitative binding affinities of drug-target pairs are differentiated as a measurement to define whether a drug interacts with a protein or not, and then a chemogenomics framework using an unbiased set of general integrated features and random forest (RF) is employed to construct a predictive model which can accurately classify drug-target pairs. The predictability of the model is further investigated and validated by several independent validation sets. The built model is used to predict drug-target associations, some of which were confirmed by comparing experimental data from public biological resources. A drug-target interaction network with high confidence drug-target pairs was also reconstructed. This network provides further insight for the action of drugs and targets. Finally, a web-based server called PreDPI-Ki was developed to predict drug-target interactions for drug discovery. In addition to providing a high-confidence list of drug-target associations for subsequent experimental investigation guidance, these results also contribute to the understanding of drug-target interactions. We can also see that quantitative information of drug-target associations could greatly promote the development of more accurate models. The PreDPI-Ki server is freely available via:

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Drug Evaluation, Preclinical / methods*
  • Genomics / methods*
  • Humans
  • Pharmaceutical Preparations / metabolism*
  • Probability
  • Protein Binding
  • Proteins / metabolism*
  • ROC Curve


  • Pharmaceutical Preparations
  • Proteins

Grant support

This work is financially supported by the National Nature Foundation Committee of P.R. China (Grants No. 21075138, No. 21275164, and No. 11271374). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.