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. 2007 Jun 1;3(6):e107. doi: 10.1371/journal.pcbi.0030107

Figure 2. PPI Network Representations of Protein Complexes.

Figure 2

(A) A hypothetical protein complex. Binary protein−protein interactions are depicted by direct contacts between proteins. Although five proteins (A, B, C, D, and E) are identified through the use of a bait protein (red), only A and D directly bind to the bait.

(B) The true PPI network topology of the protein complex.

(C) The PPI network topology of the protein complex inferred by the “matrix” model, where all proteins in a complex are assumed to interact with each other.

(D) The PPI network topology of the protein complex inferred by the “spoke” model, where all proteins in a complex are assumed to interact with the bait; no other interactions are allowed.