Hit Analyzer Panel

Hit Analyzer Panel Features

• Create Database link
• Load screening database option menu
• Reference Ligand option menu and search button
  • Reset link
  • Import button
• Filter hits section
  • Filter option menu
  • Filter definition box
    • Check box for using filter
    • Show option menu
    • Comparison tools
    • Pick in Workspace check box
    • Pharmacophore feature check boxes
    • Ion class options
    • SMARTS pattern options
  • Limit to diverse set option and text box
  • Apply Filters button
• Plot Distributions button
• Export Hypothesis button
• Display area
  • Change view option menu
  • Save Grid button
Reset button

Create Database link

Create a database from the screening results to use in the hit analysis, if the screen did not produce a database. Opens the Create Screening Database Panel.

Load screening database option menu

Load the screening database that you want to use for the analysis. The menu lists the most recently used and created databases, and a Browse item to locate any database. When the database is loaded, information from the database is used to populate the sections below.

Reference Ligand option menu and search button.

Choose the reference ligand, or click the search button to search for the reference ligand by entry title. The menu is populated with the top ligands from the database. By default, the reference ligand is the one specified in the database.

Reset link

Reset the reference ligand to the default. Only active if the reference is not the default.

Import button

Import the reference ligand into the Maestro project. The ligand is fixed in the Workspace so other structures can be used for comparison.

Filter hits section

Filter the hits by the rules in the filters specified below. Each filter is defined in a separate box, in which conditions on properties can be applied. By default, these filters are are shown: Shape similarity to reference or Screening score (depending on the screen), Pharmacophore features, Molecular properties (RDKit properties), and SMARTS patterns.

Filter option menu

Add a filter of a chosen type to the set of filters. The menu lists all available filter types, with the ones currently used grayed out. The filter types include some properties specific to shape screening, as well as molecular properties and other general properties that are stored in the database.

Filter definition box

Define a filter of a particular type by setting up conditions on properties that must be satisfied by a hit. You can add a filter definition box by choosing an item from the Filter option menu. The features available depend on the filter type, and are listed below:

Check box for using filter

Check this box to use the filter; uncheck it to disable the filter. The filter type is shown to the right of the check box.

If the reference ligand specified in the database is not selected as the reference ligand (above), the checkboxes for Shape similarity to reference and Pharmacophore features are unchecked and disabled. Clicking the Reset link checks and enables them again.

Property filter types

Show option menu

Show the list of properties available for the filter type. Clicking a property places or clears a check mark to the left of the property name. For molecular properties, there are three presets on the menu, Druglike MPO, Leadlike MPO, and Fragment MPO, which add all the relevant properties to the filter and set their values appropriately.

Comparison tools

Set up a rule for a property: choose the condition to apply to the property from the option menu and enter the value in the text box (or boxes) that the property is compared with to determine whether the property is in the desired value range. The range is shown as a slider (noninteractive) below, in terms of the range of values found in the hits.

This feature is only available for property filter types. Where there are multiple properties for a filter type (such as Molecular properties or Other properties), there is one set of these tools for each property, and there is a check box to the left of the option menu, to enable or disable the rule for the property.

Pharmacophore features filter type

Pick in Workspace check box

Check this box to pick pharmacophore features on the molecule in the Workspace, which is the reference ligand chosen above. For each feature you pick, the corresponding pharmacophore feature check boxes is checked.

Pharmacophore feature check boxes

Check the boxes for the pharmacophore features you want to use to filter the hits. Each box corresponds to a pharmacophore feature in the reference ligand.

Ion class filter type

Ion class options

Select an option for whether the hit should be basic, neutral, or acidic.

SMARTS pattern filter type

SMARTS pattern options

Select an option to Match or Exclude SMARTS patterns. SMARTS patterns can be loaded from the currently selected atoms, pasted from the clipboard, and entered/cleared manually. Click the Add Rule link to insert another row in the filter corresponding to an additional SMARTS pattern filter.

Limit to diverse set option and text box

Limit the results of the filtering to a diverse set of the specified percentage of the filtered hits.

Apply Filters button

Apply the specified filters to the hits. If you change any of the filters, click this button again to filter with the new settings.

Plot Distributions button

Plot property distributions of structures found in a hit analysis. Opens the Hit Analyzer — Plot Property Distributions Panel.

Export Hypothesis button

Export a pharmacophore hypothesis for the hits, if the Pharmacophore features filter has been applied to the hits. A file browser opens, to save the hypothesis as a .phypo file.

Display area

Display the filtered hits as 2D structures.

Change view option menu

Change various aspects of the view of the structures.

Save Grid button

Save an image of the display area as a PDF file.

Reset button

Reset the panel to its default settings.