deletions | additions       diff --git a/subsection_Virtual_Screening_Evaluation_In__.tex b/subsection_Virtual_Screening_Evaluation_In__.tex  index 8ec4ed1..47d98c7 100644  --- a/subsection_Virtual_Screening_Evaluation_In__.tex  +++ b/subsection_Virtual_Screening_Evaluation_In__.tex 
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In order to investigate the utility of the FOMS approach we consider both the ability of shape constraint filters to generate enriched subsets and the quality of shape similarity rankings generated using fragment aligned molecules. We compare to VAMS, which aligns all molecules to a canonical reference system based on their moments of inertia, and rdShape, the shape alignment module of RDKit \cite{rdkit} which dynamically aligns shapes to maximize their overlap using Open3DALIGN \cite{Tosco_2011}. The input conformers for rdShape alignment were the same aligned poses used with VAMS, and the computed similarity score is the Tanimoto coefficient.   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 a maximum  energy window cutoff difference  of 10 kcal/mol  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}. All shape queries were constructed using the reference complexes.