Examples of binding site predictions from CASP9 targets using FunFOLD. The green sticks represent residues in the model that FunFOLD has predicted as binding to the ligands. The red sticks represent residues that were not predicted or incorrectly predicted as potential ligand binding residues. The blue sticks represent the observed ligand binding site residues in the experimental structure. The white spheres represent ligands either predicted (A and C) or observed (B and D). A) An example of a good FunFOLD prediction for CASP9 target T0635 (3n1u). The predicted binding site residues and ligands are shown. The ligand cluster contains both metals and sulphates (CL-1, CA-2, SO4-2 and MG-4), with the centroid ligand predicted as MG. The red stick represents the over-prediction of residue THR69. B): The predicted binding site for T0635 using the model superposed onto the experimental structure. The observed and predicted binding site residues and the observed ligand (CA) are shown. The red sticks represent the over-prediction of THR69. C) An example where FunFOLD over-predicts to a greater extent for CASP9 target T0582 (3o14). The predicted binding site residues and ligands (ZN-1, CU-1, FE-3, FE2-1, MN-2) are shown. The centroid ligand in the ligand cluster is predicted to be ZN. D) The predicted binding site of the top model for T0582 superposed onto the experimental structure, with predicted and observer ligand binding site residues and the observed ligand (ZN) are shown.