Pose Explorer Panel

This panel uses a self-organizing map to cluster poses by sets of properties, and allows you to explore the properties of the poses based on this clustering.

A Canvas license is required (to create the self-organizing map).

To open this panel:

Click the Tasks button and browse to Receptor-Based Virtual Screening → Pose Explorer in the Task Tool.

  • Using
  • Features
  • Additional Resources

Using the Pose Explorer Panel

The project entries are clustered with self-organizing maps, using some set of descriptors, such as molecular properties, scores, or fingerprints. These clusters define groups of molecules that are similar based on the descriptors used. The number of clusters is determined by the size chosen for the map. A 3x3 map, for instance divides the entries into 9 clusters arranged in a 3 by 3 square matrix. You can calculate maps for the same set of descriptors with different sizes.

Once you have calculated a map, any property can be "projected" onto the map. To do this, you pick a property and a statistic of this property, such as the mean, maximum, or minimum. This statistic is calculated for the chosen property for each cluster in the map. These values are then displayed as a color mapping on the map. You can then explore the clusters and the property, such as which entries are in each cell, what the property values are for each cell, what the distance between cells is, and which descriptors are most important to separating the clusters.

Each cell in a property map represents a set of molecules that were grouped together in the self-organizing map. Neighboring cells are closer to each other in property space. Gray cells with an orange X are empty. The color of the cell indicates the value of the property that was mapped onto that cell.

Clicking on a cell in a property map highlights that cell and shows where the members of the cell are distributed in all the maps. By default, the size of the red circle indicates the percentage of the cell's members that are in the highlighted cell. The indicator of percentage can be changed using the Membership indicators option menu. A tooltip on the menu describes how each type of membership indicator behaves.

You can select multiple cells, using control-click. When you have multiple cells selected, the markers can represent the combined set of poses (union, logical OR), the common set of poses (intersection, logical AND), or the poses that are different (only in the first cell selected). You can choose which is represented from the Multiple cell highlight mode option menu.

When you select cells, you can apply various actions to the poses in the selected cells: select them in the Project Table, include them in the Workspace, or mark them as viewed. You can also separately mark individual poses.

Pose Explorer Panel Features

Compute Maps button

Compute self-organizing maps for the entries in the project, or, if opened from Maestro, the selected entries in the project.

Advanced button

Perform project-related actions: changing the receptor, poses, and preparing properties. Opens the Advanced Project Options Panel.

Tile button

Arrange the maps in the map area in a rectangular grid.

Cascade button

Arrange the maps in the map area on the diagonal from the top left, overlapping so that the title is showing for each map.

New Property Projection button

Add a new projection of a property to a clustering of the poses. Opens the New Property Projection Dialog Box.

Map selection option menu

This menu lists the available maps. Selecting an item places the map on top and puts focus on the map.

Plot toolbar

This toolbar allows you to configure and navigate individual plots.

See Plot Toolbar for a description.

Map area

This area displays the maps that were generated.

Each cell in a property map represents a set of molecules that were grouped together in the self-organizing map. Neighboring cells are closer to each other in property space. Gray cells with an orange X are empty. The color of the cell indicates the value of the property that was mapped onto that cell.

View Highlighted option

Show membership indicators in the cells when a cell is selected.

Use PT Selection option

Show membership markers for the poses that are selected in the Project Table (instead of the selected cells).

poses in Highlighted Cells section

This section provides options for various actions on the poses in the highlighted cells.

Select in Project Table option

Select the poses that are in highlighted cells in the Project Table, and deselect all other project entries.

Include in Workspace options

Select an option for the inclusion of poses in the Workspace. The option applies to the subsequente selection of poses: it does not change the inclusion of poses immediately.

  • All—Include all the poses in the highlighted cells in the Workspace.
  • First—Include only the first pose in the s in currently highlighted cells list in the Workspace.
  • Selected—Include only the poses that are selected in the s in currently highlighted cells list in the Workspace. When you change the selection, the poses that are included in the Workspace are changed.
  • None—Do not include any of the poses in the highlighted cells in the Workspace. This option does not exclude poses from the Workspace: it can be considered as turning off the inclusion of poses in the Workspace so that any future action has no effect on the Workspace.
Mark poses as viewed options

These options allow you to automatically mark poses as "viewed". The condition for whether a pose is "viewed " can be one of When cell is highlighted (all poses in the highlighted cell are marked), or When included in WS (poses that are included in the Workspace are considered "viewed"). A boolean property is created in the project ( Viewed) to record the viewing of the poses, and the poses are marked as viewed in the s in currently highlighted cells list.

Multiple cell highlight mode option menu

Choose what the markers represent when multiple cells are highlighted:

  • Union—Markers represent the percentage of poses in a marked cell that are in the combined set of poses (poses that are in any of the selected cells).
  • Intersection—Markers represent the percentage of poses in a marked cell that are in the set of common poses (poses that are in all of the selected cells).
  • Difference—Markers represent the percentage of poses in a marked cell that are in the first selected cell but not in any other selected cell.
poses in currently highlighted cells list

List of the titles of the poses that are in the currently highlighted cells.

Plot tips option menu

Choose what is displayed in the tool tip when the pointer is over a map cell. The choices are Cell info, which displays the cell index, the property value, cell membership, and number of members that are marked or viewed; and Distance info, which displays a 3x3 grid with cell properties in the center, and information on the distance and the largest three differences between the cell and its neighbors.

Membership indicators option menu

Choose a representation that indicates the percentage of the members of a cell that are in the selected cell:

  • By size—The size of the red dot in the cell is proportional to the percentage of the members of the cell that are in the selected cell.
  • Jet coloring—The color of the dot in the cell indicates the percentage of the members of the cell that are in the selected cell. Blue: < 20%; cyan: < 40%; green: < 60%; yellow: <80; red: <= 100%.
  • Gray scale—The shade of gray indicates the percentage of the members of the cell that are in the selected cell. White stands for 100%, black for 0%, with linear scaling inbetween. (Black is never used, because cells with 0% of the selected cell's poses are not marked.)
Mark Selected poses button

Mark the poses that are selected in the poses in currently highlighted cells list. A boolean property is added to the project ( Marked) to record which poses were marked, and the marked poses are indicated in the list. You can also use the X key to mark the selected poses.

Show 2D structure window option

Show the 2D structures of the highlighted poses in a separate window. The cells in this window contain the 2D structure and the value of the mapped property for the structure. The poses that are selected in the poses in currently highlighted cells list are marked in yellow. The pose selection can be changed in this window, and the change is reflected in the list.

Related Topics