Glide WS Model Generation Panel

Build a single trained scoring model for docking to a particular protein target, from a set of receptor-ligand complexes with binding free energy data. See the Glide WS - Model Generation Panel (Deprecated) topic for more information.

To display this panel, do one of the following:
  • click the Tasks button and browse to Receptor-Based Virtual Screening → Glide WS Model Generation
  • Features
  • Additional Resources

Glide WS Model Generation Panel Features

Use structures from option menu

Choose the structure source for the receptor-ligand complexes to use in model generation.

  • Project Table (n selected entries)—Use the entries that are currently selected in the Project Table or Entry List. The number of entries selected is shown on the menu item. When this option is selected, a Load button is displayed to the right.
  • File—Use the specified file. When this option is selected, the File name text box and Browse button are displayed.

Warning:

Attempting to load a ligand that is not a Watermap and is without a receptor will trigger an error message and the upload will fail.

Load button

Load the structures from the Project Table into the workflow and display the entries for the structures in the table.

Browse button

Click Browse and navigate to the desired file. After you open the file, the structures are imported into the project and the structure entries are listed in the table.

Clear Rows button

Clear all the rows in the table.

Table of complexes

Lists the entries for each complex loaded, with information on the receptor, ligand, binding free energy and presence of a water map. You can select a single row in the table to show details for that complex below the table.

Details for the selected complex section

Lists the Entry ID / Title, and options for the Ligand / ASL, Binding Free Energy, and WaterMap.

Entry ID / Title

Shows the entry ID and the title of the complex.

Ligand / ASL option menu

Choose the ligand if there is more than one.

Binding Free Energy option menu and controls

Set the binding free energy of the ligand to the receptor for the selected complex.

  • Value—enter the value in the text box, and click the check mark button to add the value to the table. Note: If the value entered is not within the acceptable free binding energy range (-20 to 0 kcal/mol), a validation warning message will appear and the input will not be updated.

  • Property—click the ellipsis button to open the Select Property dialog box to select the property for the binding free energy from the list of project properties, and set its units.

WaterMap option menu

Choose the source of the water map:

  • (Create)—create the water map for the complex as part of the job.

  • From File—read the water map from a file, by clicking the ellipsis button and browsing to the file in the file selector that opens.

Ligand Detection link

Open the Preferences Panel at the Ligand Detection Preferences, so you can change the settings used to detect the ligands.

Job toolbar

Manage job submission and settings. See Job Toolbar for a description of this toolbar.

The Job Settings button opens the Glide WS Model Generation - Job Settings Dialog Box, where you can make settings for running the job.

Status bar

Use the Reset button to reset the panel to its default settings and clear any data from the panel. If the panel has a Job toolbar, you can also reset the panel from the Settings button menu.

If you can submit a job from the panel, the status bar displays information about the current job settings and status for the panel. The settings include the job name, task name and task settings (if any), number of subjobs (if any) and the host name and job incorporation setting. The job status can include messages about job start, job completion and incorporation.

The status bar also contains the Help button , which opens an option menu with choices to open the help topic for the panel (Documentation), launch Maestro Assistant, or if available, choose from an option menu of Tutorials. If the panel is used by one or more tutorials, hover over the Tutorials option to display a list of tutorials. Choosing a tutorial opens the tutorial topic.

Related Topics