David Koes edited section_Search_Pharmit_provides_two__.tex  about 8 years ago

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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 adatabase  search is initiated, a right results  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, RMSD (for pharmacophore searches), similarity score (for shape searches), molecular weight,  or number of rotatable bonds; the sorting method is determined by pressing bonds. Clicking  on a result displays  the name of desired sorting method, and pressing query-aligned compound in  the name again to toggle between increasing and decreasing order. Lavender arrowheads molecular viewer. Compounds are annotated with all known database identifiers, as shown in Figure~\ref{afig}. Where applicable these identifiers are linked  to the right of the sorting method names indicate whether sorting source database, so it  is being performed in increasing (up) or decreasing (down) order. possible t