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The size of the binding pocket was measured using the Docking Simulation Module in Sybyl.
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Periodontal pockets were measured from the edge of the free gingiva to the bottom of the pocket.
Then, a binding pocket was generated.
A 10 Å sphere around the centre of the binding pocket was defined as binding pocket for the docking runs.
Furthermore, the physical binding environment of the binding pocket was evaluated using SiteMap [43, 44].
In addition, H334 residue that is structurally nearby the binding pocket was also examined.
First, the binding pocket was analyzed in the presence of the co-binding peptide using abacavir as the reference ligand.
The binding pocket was identified using Q-SiteFinder [46].
By using the built-in pocket finder, the binding pocket was identified.
The binding pocket is indicated as an exclusion surface.
The positively charged binding pocket is not big enough for ANP binding.
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