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By Cannataro M., Guzzi P.H.

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In contrast, MS-based approaches Summary 19 allow for the isolation of large protein complexes and for the detection of networks of protein interactions. However, MS-based approaches are biased toward highly abundant, stable complexes, whereas the Y2H system is particularly useful for the detection of weak or transient interactions. 1 INTRODUCTION In the real word there exist many examples of things that can be conveniently described by using a set of points or nodes and a set of lines or edges that join pairs of these points.

2 Example of a graph modeling protein interactions. The graph represents four proteins: A, B, C, and D and the interactions (A,B), (B,C), (B,D), and (C,D). proteins B and C. Such simple representation does not capture all the biological information among the interactions, for example, the kind of interactions or the kinetics. The graph can be extended with metadata associated to the edges providing a more complex representation. 2 GRAPH DATA STRUCTURES The mathematical formalism used for representing the whole set of interaction is a graph.

In this area a set of possible theoretical models to capture the global properties of these networks has been introduced that suppose a particular conformation of networks, for example, scale-free networks, or take into account global randomness. Although the presence of different models, and the definition of different measures of agreement between experimental networks and models, the low coverage of experimental techniques with respect to the real networks makes it difficult to choose one model over others.

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