Figure 5

Example of domain-domain interaction extraction. I: Given a set of protein-protein interactions (PPIs) and a protein-domain annotation scheme, PADDS transformed all PPIs into the corresponding set of domain-domain interactions (DDIs) and calculated the benefit value B _ij for all DDIs. II: The five steps involved in the DDI iterative evaluation procedure is illustrated using interactions between domains D1 and D3. III: After PADDS performed the DDI evaluation procedure for all other DDIs, the results were examined to select the final set of DDIs that can reconstitute the PPIs. P1, …, P7 denote proteins and D1, …, D8 denote domains. The benefit B _ij and the reassessed benefit $B_{\mathit{ij}}^r$ associated with the interaction between domains ij were calculated using Equations (3) and (4), respectively.