Date: 18 Jan 2008

Computational Methods For Predicting Protein–Protein Interactions

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Protein–protein interactions (PPIs) play a critical role in many cellular functions. A numberof experimental techniques have been applied to discover PPIs; however, these techniques are expensive interms of time, money, and expertise. There are also large discrepancies between the PPI data collectedby the same or different techniques in the same organism. We therefore turn to computational techniquesfor the prediction of PPIs. Computational techniques have been applied to the collection, indexing, validation,analysis, and extrapolation of PPI data. This chapter will focus on computational prediction of PPI, reviewinga number of techniques including PIPE, developed in our own laboratory. For comparison, the conventionallarge-scale approaches to predict PPIs are also briefly discussed. The chapter concludes with a discussionof the limitations of both experimental and computational methods of determining PPIs.