Molecular Biotechnology

, Volume 38, Issue 1, pp 1–17 | Cite as

Computational Prediction of Protein–Protein Interactions

  • Lucy Skrabanek
  • Harpreet K. Saini
  • Gary D. Bader
  • Anton J. EnrightEmail author


Recently a number of computational approaches have been developed for the prediction of protein–protein interactions. Complete genome sequencing projects have provided the vast amount of information needed for these analyses. These methods utilize the structural, genomic, and biological context of proteins and genes in complete genomes to predict protein interaction networks and functional linkages between proteins. Given that experimental techniques remain expensive, time-consuming, and labor-intensive, these methods represent an important advance in proteomics. Some of these approaches utilize sequence data alone to predict interactions, while others combine multiple computational and experimental datasets to accurately build protein interaction maps for complete genomes. These methods represent a complementary approach to current high-throughput projects whose aim is to delineate protein interaction maps in complete genomes. We will describe a number of computational protocols for protein interaction prediction based on the structural, genomic, and biological context of proteins in complete genomes, and detail methods for protein interaction network visualization and analysis.


Genome context Gene fusion Phylogenetic profiles Gene neighborhood Protein interaction networks Visualization 



The authors would like to thank Ronald Jansen for providing information about Bayesian network based prediction of protein–protein interactions and the graph used for Fig. 4.


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Copyright information

© Humana Press Inc. 2007

Authors and Affiliations

  • Lucy Skrabanek
    • 1
  • Harpreet K. Saini
    • 2
  • Gary D. Bader
    • 3
  • Anton J. Enright
    • 2
    Email author
  1. 1.Department of Physiology and Biophysics and Institute for Computational BiomedicineWeill Medical College of Cornell UniversityNew YorkUSA
  2. 2.Wellcome Trust Sanger InstituteHinxton, CambridgeUK
  3. 3.Terrence Donnelly Centre for Cellular and Biomolecular ResearchUniversity of TorontoTorontoCanada

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