Enrichment of PDB complexes in highest-ranking domain pairs predicted to interact. Ratio of observed/expected PDB complexes in each sample of domain pairs is plotted against cumulative rank. For example, the top 100 domain pairs ranked by E have 71-fold more PDB complexes than would be expected in 100 randomly chosen potentially interacting domain pairs in DIP. Potentially interacting domain pairs were ranked by each of three measures: S, θ and E. (a) Ranking all domain pairs by their frequency of co-occurrence in interacting protein pairs, S, yielded no significant enrichment of PDB complexes at any rank cutoff. A significant enrichment of PDB complexes was seen when domain pairs were ranked by θ, and even more so ranked by E, as shown by the successive increase in observed/expected PDB complexes at each cumulative rank. The ratio using all three measures approaches 1.0 as the number of ranked complexes approaches total number of predictions in the dataset. Our results suggest that the E score output by DPEA performs better than S or θ at identifying physically interacting domain pairs. (b) Ranking interactions of modular domains by E reveals enrichment of PDB complexes. No enrichment is found when interactions are ranked by θ or S.