Why are there three methods of specifying the Glide enclosing box center?

The different options for specifying the enclosing box center—by the ligand centroid, by the centroid of selected active site residues, and by supplied X, Y, Z Coordinates—are useful in different situations, depending on what is known about the active site. The ligand centroid option is most useful when docking new ligands to the receptor portion of a co-crystallized structure, or when using a SiteMap for the active site. The centroid of active site residues option is useful when only the approximate identity or location of the active site is known. However, this option also may be used to specify residues within a given distance of a co-crystallized ligand. When the enclosing box center is determined using a ligand or active site residues, Maestro uses this information to assign X, Y, and Z coordinates for the box center. To reproduce an enclosing box previously used for a particular receptor, you can specify exact X, Y, and Z coordinates.

Keywords: Glide, enclosing box, centroid

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