Pose Explorer — Compute Maps Panel

Compute Maps Panel Features

• Cluster Maps to Calculate section
  • Property set options
  • Name text box
  • Choose Properties button
  • Properties list
• Map Grid Size section
• Compute Maps button
• Reset Panel button

Cluster Maps to Calculate section

Choose the property sets that are to be used to cluster the poses. Five predetermined sets are available, and you can also choose a custom set. The properties that are in the predetermined set can be edited (recalculated or deleted) in the Pose Explorer — Property Preparation Panel, which you open by clicking Advanced Property Preparation.

Property set options

These options are used to select the property sets used to cluster the poses. A map is generated for each selected set. The available options are:

• Glide—Glide docking properties, which include the overall scores and the scoring terms.

• SIFT—Interaction fingerprints, which involve interactions between the ligand and the receptor. A receptor is required to generate these properties, which can also be generated in the Interaction Fingerprints panel (Discovery Informatics and QSAR → Interaction Fingerprints).

• 2D Fingerprints—Linear fingerprints with Daylight atom typing (Canvas default).

• Molecular Descriptors—Topological (Estate), semiempirical QM properties, and QikProp properties, as calculated with the Molecular Descriptors Panel (Clickclick the Tasks button and browse to Discovery Informatics and QSAR → Molecular DescriptorsClickclick the Tasks button and browse to ADME and Molecular Properties → Molecular DescriptorsClickclick the Tasks button and browse to Lead Optimization → ADME/Tox → Molecular Descriptors).

• Custom—Use a custom property set, which you specify by supplying a name and choosing properties.

Name text box

Specify the name to be used for the custom property set. The name is listed in the Cluster Maps table when you cluster the poses.

Choose Properties button

Choose the properties for the custom set. Opens a modified version of the Pose Explorer — Property Preparation Panel that does not allow addition or removal of properties, but allows you to select from the properties that are available in the project.

Properties list

List of properties that were chosen for the custom property set.

Map Grid Size section

In this section, you specify the size of the grid in the self-organizing map. The number of clusters is determined by the size of the grid. If you want to change the grid size, you must delete any existing clusters for the chosen property sets before clustering with the new grid.

Compute Maps button

Click this button to create the maps that cluster the poses. If the properties do not exist, they are calculated, and the Pose Explorer — Add Property Sets Panel opens while they are calculated. You cannot interact with this panel, and it is dismissed when the calculation finishes.

When the job finishes, an item is added to the menu on the toolbar in the main panel for each selected property set that lists the property set and the size of the map, the maps are displayed, and the remaining controls in the main panel are activated.

Reset Panel button

Reset the panel to the initial state, discarding all non-default settings.