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FOMS essentially provides a rapid means of template docking \cite{Ruiz_Carmona_2014,abagyan2015icm,Koes_2012} using shape-based scoring. The disadvantage of fragment-oriented approaches is they are critically dependent on the choice of fragment and its proper positioning in defining the query. Provided these requirements can be met, there are several advantages to shape-based fragment alignment search. By enforcing the fragment alignment, key interaction are guaranteed to be conserved. Previous results have demonstrated the importance of adding pharmacophoric properties (or `color') to shape similarity \cite{Hawkins_2007}. Fragment alignment introduces a hard bias toward matching a key portion of the query molecule without introducing any additional computation or calculation, as required by more general methods. In fact, as we have shown, pre-alignment substantially reduces the computational overhead. Prealignment, whether to fragments (FOMS) or canonical internal coordinates (VAMS) is orders of magnitude faster than methods that dynamically optimize the alignment. This holds true even if the cost to create the search database is taken into account. The time to create the databases scales with the number of molecular shapes (about 10 shapes a second on our system) and compares favorable with RDKit search (2 molecules a second).  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. 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. For cathg, Unlike whole-molecule  shape constraints provided the most meaningful virtual screening result as they could similarity, shape constraint can  select for a subshape \textit{subshape}  of the query ligand while the other methods must rank and specifically filter out potential clashes with  the full shape. receptor.