Abstract
Using the crystal structures of inhibitors bound to either group-2 or group-1 neuraminidases (NAs), AScore/ShapeDock (GaDock) scoring was shown to identify the binding modes in agreement with the experiment for all inhibitors docked in their own NA/inhibitor crystal structures. To investigate the effect of small changes in protein structure on predicted binding modes, in a set of 132 docking experiments (11 inhibitors docked in 12 group-2 NA structures), AScore/ShapeDock (GaDock) identified the correct binding modes of 116 complexes. In a total of 88 docking experiments (8 inhibitors docked in 11 group-1 NA structures), AScore/ShapeDock predicted 80 binding modes correctly. Flexible AScore/ShapeDock docking, as quite reproducible, is suggested to be convenient for designing novel H5N1 inhibitors.
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