Antibody Database - Advanced Options Dialog Box

Set options to use when importing structures into the antibody database. The options include specification of file types when importing from a directory, and setting of criteria for determining whether a structure is an antibody or not. The determination is based on sequence similarity between the candidate structure and a reference set of antibody sequence samples, evaluated separately for light and heavy chains.

To open this panel, click Advanced Options in the Antibody Database Management Panel.

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Antibody Database - Advanced Options Dialog Box Features

 

Included directories section

This section contains options that are applied when you import all relevant files from a directory.

Search for files of type options

When importing files from a designated directory, specify the file types of the files to be imported. The choices are Maestro and PDB.

Minimum sequence identity section

Specify cutoffs for determining whether a structure should be included in the database, based on percentage sequence identity. If no chain in the structure passes the tests, it is not included in the database. A chain must meet the FR threshold and either the VL or VH threshold to be included in the database.

VL (full chain) box

Specify the minimum percentage sequence identity in the light variable region for a structure to be included in the database.

VH (full chain) box

Specify the minimum percentage sequence identity in the heavy variable region for a structure to be considered an antibody.

FR subdomains box

Specify the minimum percentage sequence identity in the framework regions for a structure to be considered an antibody. This test is applied in conjunction with each of the variable region tests to determine if a chain in the structure passes: it must meet both the FR threshold and the VL threshold to be included as a variable light chain.

Framework regions used in similarity analysis section

Specify which of the four framework regions to use in the similarity analysis.

Reset button

Reset the options to their defaults.

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