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Prediction of Protein–Protein Interactions: A Study of the Co-evolution Model

  • Itai Sharon
  • Jason V. Davis
  • Golan Yona
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 541)

Abstract

The concept of molecular co-evolution drew attention in recent years as the basis for several algorithms for the prediction of protein–protein interactions. While being successful on specific data, the concept has never been tested on a large set of proteins. In this chapter we analyze the feasibility of the co-evolution principle for protein–protein interaction prediction through one of its derivatives, the correlated divergence model. Given two proteins, the model compares the patterns of divergence of their families and assigns a score based on the correlation between the two. The working hypothesis of the model postulates that the stronger the correlation the more likely is that the two proteins interact. Several novel variants of this model are considered, including algorithms that attempt to identify the subset of the database proteins (the homologs of the query proteins) that are more likely to interact. We test the models over a large set of protein interactions extracted from several sources, including BIND, DIP, and HPRD.

Key words

Protein–protein interactions co-evolution mirror-tree 

Notes

Acknowledgments

This work is supported by the National Science Foundation under Grant No. 0133311 to Golan Yona, and by the National Science Foundation under Grant No. 0218521, as part of the NSF/NIH Collaborative Research in Computational Neuroscience Program.

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Copyright information

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

Authors and Affiliations

  • Itai Sharon
    • 1
  • Jason V. Davis
    • 2
  • Golan Yona
    • 1
    • 3
  1. 1.Department of Computer ScienceTechnion - Israel Institute of TechnologyHaifaIsrael
  2. 2.Department of Computer ScienceUniversity of Texas at AustinAustinUSA
  3. 3.Department of Biological Statistics and Computational BiologyCornell UniversityIthacaUSA

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