Figure 8. Accuracy of Round 30 homodimer models predicted by protein docking methods and template-based modeling versus models derived by standard homology modeling.

The I-rms values, representing the accuracy level of the predicted interface, are plotted (vertical axis) for different models for each target (listed on the horizontal axis using the CAPRI target identification). Each point represents one model. The best models submitted by individual CAPRI predictor groups are represented by green triangles. The remaining models are those built in this study by standard homology modeling techniques⁴² on the basis of homodimer templates from the PDB. Up to 10 best models are shown per target and template category (see text). Models based on templates identified using sequence information (black triangles), models based structural alignments of individual monomers (red lozenges), and those based on structural alignments of the entire dimers (blue triangles). The targets (only dimers) are subdivided into easy and difficult targets (see text). Dashed horizontal lines represent I-rms values delimiting models of high, medium, acceptable and lower (incorrect) quality by CAPRI criteria.