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A major advantage of fragment alignment is that it enables the use of shape constraints.  Shape constraint search generally tracked or improved upon the performance of FOMS similarity ranking (e.g. Figure~\ref{cathg}). As shown in Table~\ref{pvaltable}, shape constraints were able to generate statistically significant ($p < 0.01$) enriched subsets for six of the ten targets.  Unlike whole-molecule shape similarity, shape constraint constraints  can select for a \textit{subshape} of the query ligand (i.e., perform partial shape matching \cite{Tangelder_2007})  and specifically filter out potential clashes with the receptor. Shape constraints provide a novel and unique method for specifying molecular shape queries. Since they are fragment oriented, they can be used to perform partial shape similarity search, a generaly generally  challenging problem (cite). Shape constraint searches generally took well under a second making them perfect for interactive applications. Although we have investigated automatically generated shape constraints, our assumption is that intelligently designed constraints created by human experts guided by interactive analysis of a virtual screening database would substantially outperform our interaction point based constraints. This hypothesis remains untested as intuitive interfaces that allow expert users to sculpt their desired molecule need to be developed and integrated into a comprehensive virtual screening evaluation environment.