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Rapid and Accurate Prediction and Scoring of Water Molecules in Protein Binding Sites

Figure 2

Two examples from the data set used to validate the WaterDock method.

Yellow spheres: predicted water sites, red spheres: water molecules observed in at least two experimental structures, blue spheres: water molecules observed in only one experimental structure. HIV-1 protease bound to the inhibitor KNI-272 (A). All 9 consensus water molecules and all 6 non-consensus water molecules are correctly identified. One non-consensus water molecule is in between two predictions, resulting in a false positive. This water molecule was resolved only in 3FX5 with a temperature factor of 42 Å2, so the over-prediction may be due to the uncertainty in the water molecule's position. GluR2 ligand binding core bound to AMPA (B). All water molecules within the binding site are correctly predicted.

Figure 2