Structural Modeling of Protein Interactions by Analogy: Application to PSD-95
Figure 1
Basic Steps of Comparative Patch Analysis Approach
First, the binding sites of the homologs of each domain are extracted from PIBASE and superposed on its surface. Second, for each pair of the superposed binding sites, we apply a restrained docking of the domains with PatchDock to obtain a set of candidate binary domain complexes. Each of the binary complexes is then ranked using geometrical complementarity and statistical potential, and the top-ranked complex is selected to be a final prediction.