Calculate Protein Descriptors Panel

Calculate descriptors for a protein or antibody that can be used for machine learning. These descriptors are generated for the sequences, the structures, and from a patch analysis. A full list of the descriptors is given in QSAR, AutoQSAR, descriptors, features, machine learning, ML.

To open this panel: click the Tasks button and browse to Biologics → Calculate Protein Descriptors.

  • Features
  • Additional Resources

Calculate Protein Descriptors Panel Features

Use structures from option menu

Choose the structure source for calculating the protein descriptors.

  • 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.
  • File—Use the specified file. When this option is selected, the File name text box and Browse button are displayed.
File name text box and Browse button

Enter the file name in this text box, or click Browse and navigate to the file. The name of the file you selected is displayed in the text box.

Custom Regions checkbox

Define custom regions for the calculation of the descriptors. When you check this box, a table is displayed to define the regions.

Custom regions table

This table allows you to select a region of the protein and give it a name. In the Region Name column, click the icon to edit the name. In the ASL column, click the icon to enter an ASL expression. For more information on ASL expressions, see Atom Specification Language.

Set desired system pH textbox

Set the pH value for the solution containing the protein.

Structures are antibodies options

Select Yes if the structure is an antibody. The Use numbering scheme option menu is displayed.

Use numbering scheme option menu

Choose the numbering scheme for the antibody, from Chothia, Kabat, IMGT, EnhancedChothia, or AHo.

Job toolbar

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

The Job Settings button opens the Calculate Protein Descriptors - Job Settings Dialog Box, where you can make settings for running the job.

Calculate button

Run the job to calculate protein descriptors.

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.

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