Phase Ligand Screening Panel

Screen ligands against one or more pharmacophore hypotheses.

To open this panel, click the Tasks button and browse to Ligand-Based Virtual Screening → Ligand Screening.

  • Using
  • Features
  • Additional Resources

Using the Phase Ligand Screening Panel

This panel allows you to screen a set of ligands for matches to one or more pharmacophore hypotheses. 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 X Dialog Box, by right-clicking on a hypothesis in the Workspace, or clicking on the button in the Structure Hierarchy for the hypothesis feature.

If you are screening a database, the feature definitions for the hypothesis may differ from those in the database. In this case, new features are temporarily generated for the ligands during screening, based on the definitions for the hypothesis.

The output from a screening run against a single hypothesis is a single entry group, named jobname_hypothesis, with the hypothesis as the first entry in the group. When multiple hypotheses are used, the output consists of a single entry group named jobname, with subgroups for the hits for each hypothesis, named hypothesis. The hypothesis is included as the first entry in each subgroup. If multiple databases were screened, there is a property that records the name of the database.

To write out the input file and a script for running the job from the command line, click the arrow next to the Settings button and choose Write. For information on command usage and options, see phase_screen Command Help and Searching for Matches with phase_screen.

Phase Ligand Screening Panel Features

Ligands to screen option menu

Choose the source of ligands for screening.

  • Phase Database—Choose one or more Phase databases for screening. The database table and tools for adding and deleting databases are displayed.
  • Project Table (selected entries)—use the selected entries in the Project Table. The number of entries is reported below this option menu.
  • File—Select a file for screening. The file name text box and Browse button for selecting the file are displayed.
Database table

Lists the databases chosen for screening. The table columns are described below.

Use Column of check boxes to mark a database for use in screening.
Database Name of the database.
Subset Displays the subsets available in the database in an option menu. If you choose None, the entire database is screened; if you choose a subset, only the chosen subset is screened. This column shows N/A if the database is a remote database.
Add Database option menu

Choose the location of the database from this option menu, and add a row to the table with the database information.

  • Browse—browse the file system for a database. Opens a file selector so you can locate and select the database.
  • Remote database—use a database that is only accessible remotely (e.g. on the host on which the job will be run). Opens a dialog box in which you can specify the path to the database. No checking is done on the existence of the database, so you must make sure it exists in the specified location on the remote host before you submit a job.
Delete button

Delete the selected database from the table.

File name text box and Browse button

Click Browse to navigate to and select the ligand file to screen. The name of the file is displayed in the text box (which is noneditable), and the number of ligands in the file is displayed below.

Hypothesis selection

Specify the hypotheses against which you want to screen the ligands. You can screen against multiple hypotheses simultaneously.

Pharmacophore models with more than about 8 features can increase screening resource requirements substantially.

Add Hypothesis option menu

Add hypotheses that you want to screen against 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.

You can also add hypotheses to the table from the Entry List, by clicking the H button and choosing Next Steps → Add to Database Screen.

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. The columns are described below.

Hypothesis Name of the hypothesis.
Matches Minimum number of features that are required to match the hypothesis. Click the arrow to choose the minimum number from a list. Setting it to a smaller number than the total number of features in the hypothesis (also shown) allows partial matches to be accepted as hits.
Excluded Volumes If a hypothesis has excluded volumes, a check box is displayed in this column. Check this box to apply the excluded volumes in the screen.
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, 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 Phase Ligand Screening - 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.

Tutorials

Related Topics