Figure 3

We clustered all the 153127 interface fragment pairs in the 3did database using different values of RMSD cutoff. The derived numbers of clusters under different RMSD values are plotted in (a). Based on these statistical results, a cutoff value of 4 Angstrom was chosen in the following studies. This results in a totle number of 2135 clusters. We counted the number of fragment pairs in these 2135 clusters and ranked them in decreasing order (b). We show that fragment pairs are not uniformly distributed in all clusters. A small number of clusters are highly abundant. As a result, only clusters with more than 20 members were considered, leading to the library of 459 highly representative entries. These 459 clusters cover more than 90% interface fragment pairs from the whole database.