David Koes 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.  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{openbabel}. \cite{O_Boyle_2011}.  \subsection{Result Browser}  When a database search is initiated, a right sidebar opens to display the search results. This sidebar may be hidden by pressing the right-facing arrow at the top left of the sidebar, or it may be closed by pressing the "x" in the upper right corner. Results may be sorted in increasing or decreasing order based on RMSD, mass, or number of rotatable bonds; the sorting method is determined by pressing on the name of desired sorting method, and pressing the name again to toggle between increasing and decreasing order. Lavender arrowheads to the right of the sorting method names indicate whether sorting is being performed in increasing (up) or decreasing (down) order.