deletions | additions       diff --git a/subsection_Shape_Constraints_Since_we__.tex b/subsection_Shape_Constraints_Since_we__.tex  index 006dffa..310626b 100644  --- a/subsection_Shape_Constraints_Since_we__.tex  +++ b/subsection_Shape_Constraints_Since_we__.tex 
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For visualization purposes we display the \textit{inverse} of the maximum shape, which corresponds to the region of space the desired shape is excluded from, to more clearly visualize the minimum shape, which is, by definition, fully subsumed in the maximum shape.  Similarily, the ligand shape can be used to develop a minimum shape constraint. However, constructing a minimum shape constraint directly from the ligand shape, even if the shape is shrunk or skeletonized, results in a highly specific shape query that may be limited in its ability to retrieve novel chemical scaffolds.  As an alternative to directly using the shape of a bound ligand, we derive \textit{interaction points} from the ligand-receptor complex. Interaction points are points at the center of clusters of ligand atoms that are interacting with the receptor. Interacting ligand atoms are defined to be those no more than 6{\AA} away from a receptor atom, as measured between atom centers. These atoms are then clustered into groups of three or more that are no more than 4{\AA} across. The center of the cluster is an interaction point. An example of interaction points identified from a ligand-receptor complex is shown with the corresponding minimum and maximum shape constraints in Figure~\ref{iptsshape}. Interaction points provide a more  general specification of the binding mode of a ligand that is less dependent on the ligand chemical scaffold than the full ligand shape and ignores non-interacting components of the ligand.