Interfaces in molecular docking

The Fast Atomic Density Evaluation (FADE) program analyzes shape complementarity using atomic density methods and fast Fourier transforms (FFT). Statistical results for 184 protein-protein and protein-DNA complexes are presented. Almost all of the interfaces studies were found to be complementary, and the average FADE complementarity score highlighted systems known to have strong shape complementarity at the binding interfaces. Also given is a detailed analysis of the interfaces for Fasciculin-Acetylcholinesterase and Barnase-Barstar to show how shape complementarity relates to site mutagenesis experiments. For these two cases, there was good agreement between interface points of highest complementarity and the location of residues known to be important for binding.