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    • Hit List and Query Management

    • Presenter: Jesse Gordon , Company: PerkinElmer Informatics
    • Duration: 9 min
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  • Use the Queries tree to track history of searches between sessions, allow queries to be rerun or reconstituted, and merge lists by drag-and-drop. Queries color-coded to relate to ChemBioViz plots.

    The "Queries" tab in ChemBioFinder's Explorer Window shows a history of queries run in the current session of ChemBioFinder, as well as ones saved from previous sessions. The queries themselves can be used to create new merged queries by drag-and-drop of one query on top of another. You will then see a "Restore/Merge List" window which allows you to intersect the two lists (find the substances which are in common between the two lists ), subtract them (find the substances in the first list which are not in the second list), or find the union of the two (sum the two lists together). This video clip demonstrates a series of queries exemplifying the usage of intersections and subtraction merges. The steps are:

    • Start with a sample list of 319 molecules (available for download below), containing typical substances of mixed types.
    • On the Search menu, select Enter Query and search for a benzene substructure, resulting in 132 substances in the query result.
    • The query is labeled "Q1* [132] (SSS [query=C6H6]), which means "Query #1 resulted in 132 substances, from a substructure search for benzene".
    • The benzene moiety is highlighted in red for each substance on the results list (if there are two benzene substructures in one substance, only one is highlighted).
    • Run another search, for Molecular Weight > 200; this results in 104 substances in the query result, labeled "Q2* [104] (Molweight: > 200)".
    • Now run the same two queries together as one query: draw benzene in the Structure field, and "> 200" in the Mol. Weight field, then click Search. This results in: "Q3* [56] (SSS[query=C6H6]+Molweight:>200)". Fifty-six molecules meet both criteria, a benzene substructure and MW < 200.
    • Now let's rerun that same two-criteria query using the graphical interface: drag-and-drop Q1 onto Q2, then pick "Intersect [L1 and L2]". The result is: "Q4* [56] (Q1 and Q2)".
    • Note that the graphical interface result Q4 is the same list of 56 substances as the double-criteria result Q3, just easier to understand and run.
    • Now let's create an intersection that could not be done with manually-entered criteria. Select menu item Search > Find Structures > Classes > Aromatics > 4n+2. This results in: "Q5* [169] (Find aromatics)".
    • Run a second class search, for metals: Select menu item Search > Find Structures > Classes > Metals. This results in: "Q6* [20] (Find metals)".
    • Now make the intersection of the two: drag-and-drop Q5 onto Q6, then pick "Intersect [L1 and L2]". The result is: "Q7* [10] (Q5 and Q6)", which means ten substances include both a metal and an aromatic substructure.
    • Note that locating metal aromatics would be an overly complicated query using manually-entered criteria. The graphical method hence allows for more complicated queries than are possible with manual entry.
    • Finally, let's try a subtraction. Drag-and-drop Q5 (aromatics) onto Q1 (benzene), then select "Subtract [L1 minus L2]", resulting in: "Q8* [37] (Q5 minus Q1)", which means 37 molecules are aromatic but do not contain a benzene substructure (they are furans, pyridines, and so on).

    Users can double-click on a query result to bring the results of that query back to the Form View list for viewing. Any of the search results could be output as an SDfile, for use in other programs like ChemDraw/Excel. Hence the list management tools make ChemBioFinder a powerful selection tool for managing chemical data.

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      • Sample list of 319 molecules: sdf file