Jocelyn Sunseri edited section_Search_Pharmit_provides_two__.tex  about 8 years ago

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Pharmit allows users to specify additional, non-structural filters on the results. The number of compounds returned can be reduced by restricting the number poses returned for every conformation, the number of conformations returned for every compound, and the total number of compounds.  Compounds may be filtered by specifying desired ranges for molecular properties that are commonly used to identify drug-like molecule.  As shown in Figure~\ref{afig}, Figure~\ref{shapefig},  these include molecular weight, the number of rotatable bonds, LogP (a measure of lipophilicity), polar surface area (indicative of ability to permeate cell membranes), the number of aromatic groups, the number of hydrogen bond acceptors, and the number of hydrogen bond donors. Properties are precomputed using OpenBabel \cite{O_Boyle_2011}. \subsection{Result Browser}  When a search is initiated, a results sidebar opens to display the search results, as seen in Figures~\ref{afig} Figures~\ref{pharmfig}  and \ref{anotherfig}. \ref{shapefig}.  Results may be sorted in increasing or decreasing order based on RMSD (for pharmacophore searches), similarity score (for shape searches), molecular weight, or number of rotatable bonds. Clicking on a result displays the query-aligned compound in the molecular viewer. If desired, a new Pharmit session can be initiated from the ligand-protein complex represented by the selected hit compound. Compounds are annotated with all known database identifiers, as shown in Figure~\ref{afig}. Figure~\ref{shapefig}.  Where applicable these identifiers are linked to the source database, so it is possible to immediately investigate bioactivity data in PubChem or bring up the order page from a commercial vendor.