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Computational Prediction of Protein–Protein Interactions

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Abstract

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.

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Acknowledgment

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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Authors and Affiliations

  1. Department of Physiology and Biophysics and Institute for Computational Biomedicine, Weill Medical College of Cornell University, 1300 York Avenue, New York, NY, 10021, USA

    Lucy Skrabanek

  2. Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK

    Harpreet K. Saini & Anton J. Enright

  3. Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Room 602, M5S 3E1, Toronto, ON, Canada

    Gary D. Bader

Authors
  1. Lucy Skrabanek
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  2. Harpreet K. Saini
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  3. Gary D. Bader
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  4. Anton J. Enright
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Corresponding author

Correspondence to Anton J. Enright.

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Skrabanek, L., Saini, H.K., Bader, G.D. et al. Computational Prediction of Protein–Protein Interactions. Mol Biotechnol 38, 1–17 (2008). https://doi.org/10.1007/s12033-007-0069-2

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  • DOI: https://doi.org/10.1007/s12033-007-0069-2

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