Examples of protein binding site predictions. Network representation of three proteins shown as balls (nodes) and sticks (edges connecting nodes). Nodes are colored by their closeness value (from minimum values in blue to maximum values in red). All partner proteins are shown in green ribbon. (A) A successful prediction for the receptor of the enzyme/inhibitor complex between Substilisin and Streptomyces subtilisin inhibitor (PDB code 2SIC). The top four residues according to the closeness parameter are part of the interface where the ligand binds. (B) Prediction for the receptor of antibody/antigen between the camel VHH and Pancreatic alpha-amylase (PDB code 1KXQ). The prediction is unsuccessful because residues with high closeness values are in the protein core, far from the binding site. (C) Ligand of the "other" type complex between CDK2 kinase and the human cyclin dependent kinase subunit (PDB code 1BUH), in which all four predicted residues are in the binding site.