Hypothesis Validation Panel

Validate one or more hypotheses by running a screen on a set of active ligands and decoy ligands. The results of the validation can be viewed in the Enrichment Viewer Panel.

To open this panel, you can:

  • click the Tasks button and browse to Ligand-Based Virtual Screening → Hypothesis Validation
  • click the H button in the Entry List for a hypothesis and choose Next Steps → Validate Hypothesis
  • click the Workflow Action Menu button in the Entry List for a hypothesis group and choose Validate Hypotheses
  • Using
  • Features
  • Additional Resources

Using the Hypothesis Validation Panel

This panel allows you to validate one or more pharmacophore hypotheses by using them to screen a set of active and decoy ligands to determine how well the actives are enriched in the screening. The panel provides the tools for setting up a screen with the default settings and control over the number of features matched. Options for conformer generation, feature equivalence, scoring, constraints, cutoff criteria, and output can be made in the Screening Settings Dialog Box.

Options for individual features of a hypothesis, such as required, allowed, and forbidden matches and feature-matching tolerances are properties of the hypothesis itself. You can set these properties in the Edit feature dialog box, by right-clicking on a hypothesis in the Workspace.

When the job finishes, you can view the enrichment results in the Enrichment Viewer Panel. A banner offers a link to open this panel with the results of the job loaded.

Hypothesis Validation Panel Features

Load active and decoy sets text boxes and browse buttons

Load the active ligands and the decoy ligands for the validation, from files. Enter the file name in the appropriate text box, or click the browse (…) button to navigate to the file.

Hypothesis selection

Specify the hypotheses that you want to validate. You can validate multiple hypotheses simultaneously.

Add Hypothesis option menu

Add hypotheses that you want to validate to the table. The option menu allows you to choose the source of the hypotheses:

  • Workspace—Add the hypothesis that is displayed in the Workspace.
  • Project table (selected entries)—Add the hypotheses that are selected in the Project Table
  • File—Add hypotheses from a hypothesis file. Opens a file selector, in which you can load hypotheses from a file (.phypo for a file with a single hypothesis or _phypo.maegz for a file with multiple hypotheses). You can select multiple files, and all hypotheses are read from the files you select.

If you opened the panel from the Workflow Action Menu button in the Entry List, the relevant hypotheses are preloaded into the table. You can use the Workflow Action Menu button to add more hypotheses to the table.

Delete button

Delete the selected hypotheses from the table.

Hypothesis table

This table lists the hypotheses. You can select multiple hypotheses to delete from the table.

If a hypothesis has excluded volumes, a check box is displayed in the Excluded Volumes column. Check this box to apply the excluded volumes in the validation.

Hits must match at least N features text box

Minimum number of features required for a match. This must be no greater than the number of features in the hypothesis. Setting it to a smaller number allows partial matches to be accepted as hits.

Prefer partial matches of more features option

If this option is selected, matches involving fewer than n features will not be sought if there are any matches with n features. This option is only available if you are matching less than the maximum number of features.

Screening Settings button

Make settings for screening the structures for the validation, including conformer generation, feature type equivalence, scoring function, constraints on specific feature arrangements, cutoffs for rejecting matches, and amount and format of output. Opens the Screening Settings Dialog Box.

Job toolbar

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

The Job Settings button opens the Hypothesis Validation - Job Settings Dialog Box, where you can make settings for running the job.

Status bar

The status bar displays information about the current job settings and status for the panel. The settings includes 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.

Use the Reset button to reset the panel to its default settings and clear any data from the panel. You can also reset the panel from the Job toolbar.

The status bar also contains the Help button , which opens the help topic for the panel in your browser. If the panel is used by one or more tutorials, hovering over the Help button displays a button, which you can click to display a list of tutorials (or you can right-click the Help button instead). Choosing a tutorial opens the tutorial topic.

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