Cluster Hit List Poses from Gigadock

Locate the Cluster Poses floe as follows.

  1. Click on the ‘Floes’ button in the left menu bar

  2. Click on the ‘Floes’ tab in the upper left of the main window.

  3. Click ‘All Floes’ in the left pane

  4. In the search bar at the top of the right pane enter Cluster Poses

The Cluster Poses floe will be visible to the right. Click on it to bring up the launch Job Form and set the following parameters

  • Jobs Properties

    • Output Folder : Tutorial/My Data/HSP90 Dock

  • Promoted Parameters

    • Inputs

      • Input Dataset : Tutorial/My Data/HSP90 Dock/Hit List

        1. Click the ‘Choose Input’ button for Input Folder to open the Select Dataset modal.

        2. Click the ‘Input Data’ folder.

        3. Select the Hit List dataset

        4. Click ‘Use dataset as Input’

    • Outputs

      • Output Dataset : Pose Clustered Gigadock Hit List

Once the parameters are set scroll to the bottom of the page and click ‘Start Job’. The job will take ~1.5h and include an Orion compute charge of ~$5. Wait for the floe to complete before continuing with the tutorial.

View Results

Setup Basic View in 3D Window

Make the docked molecules and the structure they are docked to active as follows.

  1. Go to the Project Data page by clicking on the blue ‘Data’ button on the left menubar.

  2. Select ‘My Data’ under ‘Project Data’ from the list of options to the left of the page.

  3. Select the ‘HSP90 Dock’ Folder in the main window.

  4. In ‘Type’ drop down menu in the top center check ‘Datasets’ if it is not already.

  5. Clicking on ‘Active Datasets’ menu in the upper right. If any dataset are active click ‘Clear All’ in the menu.

  6. Locate the dataset named Receptor and make it active by clicking on the greg circle with the plus symbol to the left of the name. The grey circle will turn green.

  7. Locate the dataset named Pose Clustered Gigadock Hit List and make it active by clicking on the grey circle with the plus symbol to the left of the name. The grey circle will turn green.

Now move to the 3D window and setup the view

  1. Click on the ‘3D’ button on the left menu bar and do the following in the ‘All Data’ window.

  2. Click the faint grey dot to the right of ‘1UGY(A) > PU(A-1224)’. It will turn green.

  3. Expand the tree under ‘1UGY(A) > PU(A-1224)’ by clicking on the chevron immediately to the right of the name.

  4. In the newly expanded tree expand the tree under DU’1UGY(A) > PU(A-1224)’ by clicking on the chevron immediately to the right of the name.

  5. In the newly expanded tree click on the left arrow to the left of L’PU2(A-1224)’ and in the menu that opens click the ‘Style’ button.

  6. In the Styling menu that appears under ‘Color by’ click green to color carbon atoms of the crystallographic ligand green.

  7. Click outside of the Styling menu to close it.

  8. Click on the first molecule under ‘Gigadock Pose Clustered Hit List’

Click on the first molecule of the hit list to see it in the context of the active site in the 3D view. The next or previous molecule can be viewed using the up/down arrows. Any interesting molecules can be pinned using the space bar, and will appear in the top left list that was set to show ‘Pinned Molecules’. The pinned molecules can be saved using the save button in lower left of ‘Pinned Molecules’ pane.

View Pose Cluster Heads Only

  1. Click the ‘Filters’ button in the upper left to open the filtering down menu.

  2. Clear any existing filter by clicking on the x to the right of each existing filter in the opened drop down menu

  3. In ‘New Filter From’ select ‘Pose Cluster Tanimoto’

  4. Choose 1.0 as the minimum value for ‘Pose Cluster Tanimoto’

Only the cluster heads will now be visible in the 3D window

View Top 5 Scoring of Each Cluster Only

  1. Click the ‘Filters’ button in the upper left to open the filtering down menu.

  2. Clear any existing filter by clicking on the x to the right of each existing filter in the opened drop down menu

  3. In ‘New Filter From’ select ‘Pose Cluster Rank’

  4. Choose 5 as the maximum value for ‘Pose Cluster Rank’

Only the top 5 scoring poses in each cluster will now be visible in the 3D window

View One Pose Cluster Only

  1. Click the ‘Filters’ button in the upper left to open the filtering down menu.

  2. Clear any existing filter by clicking on the x to the right of each existing filter in the opened drop down menu

  3. In ‘New Filter From’ select ‘Pose Cluster ID’

  4. Choose 10 as the maximum and minimum value for ‘Pose Cluster ID’

Only poses from cluster 10 will now be visible.

Note

The choice of cluster 10 is arbitrary. This filter can be applied with any cluster ID.