Figure 3

Examples of known binding sites and destabilizing regions identified in 3 proteins. Each protein is represented twice: its binding sites (residues colored green) and ligands (displayed and colored as cpk) are shown on the left panel, whereas destabilizing regions (residues colored orange or cyan) are shown on the right panel. Represented residues are all displayed as "balls-and-sticks". Ligands considered as biologically irrelevant are displayed on each panel as balls-and-sticks and colored cpk. Pdb ids used to reference subfigures are those used in the text and tables. (a) Endoglucanase B (Pdb id 1qi2 and 1qhz used for left and right panels, respectively), a protein with a polysaccharide-binding site. Backbone is displayed as coil and colored grey. PPV = 34.5%, Sensitivity = 71.4%. Two destabilizing regions are detected in this protein (one in orange and the other in cyan). (b) Phytase (Pdb id 1h6l and 2poo used for left and right panels, respectively), a protein with a small ligand-binding site. The backbone is displayed as cartoons and colored grey. PPV = 40.0%, Sensitivity = 62.5%. Two destabilizing regions are detected in this protein (one in orange and the other in cyan). (c) AML-1 (Pdb id 1h9d and 1eao used for left and right panels, respectively), a protein with a protein-binding site and a nucleic acid-binding site. The bound protein, CBF-β, is represented as cartoons and colored dark-red. AML-1 is displayed as coil and colored grey. No destabilizing region was detected in this protein. Figures 3 and 5 were drawn with Molscript [77] and rendered with Raster3D [78].