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For each target, conformers of the active and decoy compounds were generated using rdkit\cite{rdkit}. A maximum of 100 conformers with a minimum RMSD difference of 0.7{\AA} and an energy window cutoff of 10 were generated for each compound. For each fragment considered, the corresponding conformers were extracted into fragment-specific subsets. The subsets were then preprocessed to create VAMS and FOMS search databases. The VAMS database stores a single pose for each conformation aligned along its moments of inertia. For FOMS, if a compound contains multiple instances of the anchor fragment or the fragment contains symmetries, multiple poses per a conformation are stored to account for the multiple fragments/symmetries.  For each target, a single reference structure was identified by searching BindingDB,\cite{Liu_2007} PDBbind,\cite{Wang_2005} and Binding MOAD\cite{Hu_2005} for the complex with the best binding affinity. The structures were visually inspected to identify buried anchor fragments that made key contacts with the protein, as shown in Figure~\ref{targets} and Table~\ref{fragtable}.  \textbf{shape constraint generation}