Antibody Database Management Panel

In this panel you can create and edit antibody databases, export data, and set the default database to use for prediction tasks.

To open this panel, click the Tasks button and browse to Biologics → Antibody Database Management.

  • Using
  • Features
  • Additional Resources

Using the Antibody Database Management Panel

In this panel you can create a new antibody database or update an existing database.

The structures that are added to a database are filtered, so that only those structures that have sufficient sequence similarity to a reference set of antibodies are included. The similarity is evaluated and applied separately for light and heavy chains, so a structure can be included with just a light chain match, for example. The similarity in the variable and framework regions are tested independently, with different thresholds, and both must be met for a chain to be included.

When you first open the panel, the default database is loaded. Normally this database is installed by an administrator and you do not have write privileges, so it is opened read-only. You can import this database into your own database if you want, as described below. It is only necessary to do this if you want to modify the data in some way, because you can specify multiple databases for modeling.

Antibody Database Management Panel Features

 

Database file text box

The path to the current database is shown in this noneditable text box.

Open/Create button

Open an existing database or create a new database (.db file). Opens a file selector, in which you can navigate to a location and choose a database to open or provide a name for a new database.

Antibody table

This table lists all the antibodies in the database. The PDB ID is given as the row label, rather than an index. The columns in the table give the chain names of the heavy and light chains, the identity and length of the six loops, the light chain type, information from the PDB (title, ID, deposition date, format version, R, Rfree, resolution, species, author, method), the date added to the database, the file name, whether the ligand is present, and comments.

Table filter text box and buttons

Filter the table by searching for strings in the table and only showing the rows that contain the string. By default, all visible text is searched, but you can change it by clicking Select and choosing the columns you want to search on. To return to sorting all visible columns, click Reset. The text box has a tool tip that explains the syntax for the search string, which can include relational operators, wildcards, regular expressions, and some special terms.

Update Database button

Updates the database format without changing the contents if you are using an older format. Additionally, you can add and delete antibody entries from a custom antibody database.

Show columns options

Show all columns (All) or a small subset of columns (Subset), which comprises Light Chain Type, PDB ID, Date Added, and Species.

Delete buttons

Delete the rows that are selected in the table (Delete Selected Rows) or delete all the rows in the table (Delete All Data). Delete operations cannot be undone.

Export Table button

Export the data in the table to a CSV file. Opens a file selector, in which you can navigate to a location and name the file.

Add Selected to menu

Export structures in the selected rows to either the Project Table, the MSV (Sequences Only), or to both the Project Table and MSV. Choosing an option will open the structures in a new tab.

Add structures to database buttons

Add structures to the database, subject to the filtering procedure described above. The possible sources are:

  • Workspace—import structures from the Workspace.
  • Files—import structures from PDB or Maestro files. Opens a file selector, in which you can navigate to and select multiple PDB files.
  • Directory—import all structures from a directory. Opens a directory selector, in which you can navigate to the directory to import from.
  • Database—import structures from an existing database. Opens a file selector, in which you can navigate to and select the database (.db) to import from. Import progress is displayed in a bar at the bottom of the panel.

You can set options for adding structures to the database in the Antibody Database - Advanced Options Dialog Box, which you open by clicking Advanced Options. These options are for file types, minimum sequence identity, and framework regions used for similarity analysis.

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