Antibody Loop Modeling Panel

Predict CDR loops in an antibody using Prime loop prediction.

To open this panel: click the Tasks button and browse to Biologics → Antibody Loop Refinement.
To open this panel from the entry group for the results of an antibody structure prediction job, use the Workflow Action Menu .

  • Using
  • Features
  • Additional Resources

Using the Antibody Loop Modeling Panel

In this panel, you can run a Prime loop prediction job for a single loop of the input antibody. See Refining Protein Structures for more information; technical information can be found in Loop Refinement Technical Details.

If you opened this panel from the Antibody Structure Prediction Panel, the antibody model structure is already defined, and the tools for selecting structures are unavailable. The only task is to select the loop and run the job. Otherwise you can load structures into the panel, then select each structure you want to run and choose a loop for it, and run the job. This is useful if you ran a batch prediction of antibody structures and want to refine loops in all of them, for example.

If you want to predict multiple loops in the same antibody, the predictions have to be run sequentially, i.e. the output structure from one job is used as the input structure from the next. If you opened this panel from the Antibody Structure Prediction Panel, you will have to close this panel and reopen it (from the WAM for the loop prediction or from the Task Tool) to do this, because the antibody structure and template structure selection tools are not available. The Refine Loops Panel provides options for running the sequential refinements of multiple loops in a single job.

When a job is run with multiple structures, subjobs are created for each structure and can be run simultaneously.

Antibody Loop Modeling Panel Features

If this panel is opened from the Antibody Structure Prediction Panel, the structure source and structure selection features are not available, as the structures are predefined.

Use structures from option menu

Choose the structure source for antibody loop modeling.

  • 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. An icon is displayed to the right which you can click to open the Project Table and select entries. When this option is selected, a Load button is displayed to the right.
  • Workspace (n included entries)—Use the entries that are currently included in the Workspace, treated as separate structures. The number of entries in the Workspace is shown on the menu item. An icon is displayed to the right which you can click to open the Project Table and include or exclude entries. When this option is selected, a Load button is displayed to the right.

Not available if the panel was opened from the Antibody Structure Prediction Panel.

Open Project Table button

Open the Project Table panel, so you can select or include the entries for the structure source.

Not available if the panel was opened from the Antibody Structure Prediction Panel.

Load button

Load the structures from the Project Table or Workspace into the panel.

Not available if the panel was opened from the Antibody Structure Prediction Panel.

Select structures list

Select the structures to use for predicting the loops in the antibody model, by clicking the boxes. When you check a box, the row is selected and the loops for the selected structure are displayed in the Select loop for prediction table. If you click elsewhere in the row, the structure is selected and the loops displayed but the check box does not change. This allows you to view the loop list without selecting the structure for loop prediction.
The structure from the Antibody Structure Prediction Panel is shown as the only structure if the panel was opened from there, and cannot be changed.

Apply Numbering Scheme option menu

Choose the numbering scheme to use, from Chothia, Enhanced Chothia, Kabat, IMGT, AHo. The definition of the CDR loops, ranking of frameworks, CDR loop clustering, and choice of loop templates are affected by the numbering scheme. These differences can lead to different predicted structures.

Select loop for prediction table

This table lists the loops available for prediction for the selected structure. You can select a single loop for prediction. If you want to predict more than one loop for a given structure, you will need to run the jobs sequentially, with the results from each job as input to the next. If you switch to another structure, the loop choice for the previous structure is remembered. This allows you to make a loop choice for multiple structures.

Job toolbar

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

The Job Settings button opens the Antibody Loop Modeling - 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.

Tutorials

Related Topics