A well studied protein complex is chosen to see how many true interactions could be discovered inside it. Because the size of protein complex is much smaller than the whole PPI network, we could test every possible links and select the most reliable ones.  

In the experiment, we select Saccharomyces cerevisiae 26S Proteosome Complex as a case to study. Out of the 36 proteins in Proteosome Complex, 34 proteins could be found in our dataset. This complex is selected because it is well studied and has 3D interaction information in PDB database. 

Saccharomyces cerevisiae 26S Proteosome Complex contains 36 proteins in BIND database. It also contains 4 structures in PDB covering 13 proteins and 23 physical interactions, only 1 exists in our dataset.  

In the experiment, IRAP* detects 45 interactions between 13 proteins: 14 of these are the physical interactions recorded in PDB (c.f. 1 exists in the original dataset); another 12 are experimentally detected interactions in BIND only; 19 new interactions are also predicted.