Inferring Protein-Protein Interactions (PPIs) Based on Computational Methods
Protein-Protein Interactions - Computational and Experimental Tools
Introduction Proteins are involved in many essential cellular processes, such as metabolism and signalling. They function by interacting with other molecules within the cell. Thus, protein interaction is one of the important keys to understand protein functions. As a consequence of the development of high-throughput experimental methods for detecting protein interactions, large volumes of data are now available. Although the data are valuable, there are limitations to their application.
... pplication. Therefore, computational methods are helpful tools for predicting protein interactions. With the increase in genome sequence data, the importance of computational methods in this field is growing more and more. Another important factor to understand protein function is flexibility, because a protein molecule is not a rigid body. Flexible regions are often necessary for proteins to perform their functions, e.g. by enabling their flexible conformations to interact with other molecules and proteins. Therefore, it is important to understand the relationship between protein flexibility and protein interactions. In accordance with the increasing numbers of available protein structures, several databases that deal with protein flexibility have been built. Computational methods for analyzing protein motion are also being developed, for applications to PPI (protein-protein interaction) data. The aim of this chapter is to provide a review on PPI prediction by computational techniques. In the first half of this chapter, the concepts and applications of several methods for inferring PPIs are introduced. They use genomic information based on evolutionary events. In the second half, the databases and prediction methods that deal with protein flexibility are introduced, and the possibility of inferring PPIs from protein flexibility will be discussed.