Chemogenomics pp 225-247 | Cite as

Network and Pathway Analysis of Compound–Protein Interactions

  • Richard J. Brennan
  • Tatiana Nikolskya
  • Svetlana Bureeva
Part of the Methods in Molecular Biology book series (MIMB, volume 575)


We describe an integrated system that brings together predictive chemical analyses based on compound structure, knowledge bases of chemogenomics data associating compounds to biological, pharmacological and toxicological properties, and a systems biology functional data analysis and network reconstruction approach, to provide an in silico evaluation of the possible effects of xenobiotics on biological systems. We demonstrate the combination of drug and xenobiotic metabolism prediction, quantitative structure-activity relationship (QSAR) models and structural similarity searching to generate a list of similar compounds to, and possible targets for novel compounds. These lists of compounds and proteins are mapped to functional ontologies such as gene-disease associations, biological processes, and mechanisms of toxicity, and can be used to reconstruct biological networks linking together the component nodes into biologically-meaningful clusters. Thus, an assessment of biological effects can be made early in the discovery and development process that can be used to prioritize the best compounds for additional testing or development, or to direct efforts in medicinal chemistry to improve compound activity profiles.

Key words

Structural similarity search Target prediction Functional analysis Pathway analysis Network reconstruction 


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Copyright information

© Humana Press, a part of Springer Science+Business Media, LLC 2009

Authors and Affiliations

  • Richard J. Brennan
    • 1
  • Tatiana Nikolskya
    • 1
  • Svetlana Bureeva
    • 1
  1. 1.GeneGo Inc.EncinitasUSA

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