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Project Management

Effective data organization is crucial for managing antibody campaigns. AbLead uses Projects to group related sequences and structures.

Creating a Project

  1. Navigate to the Dashboard.
  2. Click File > Import Project.
  3. Enter a descriptive Project Name.
  4. (Optional) Add Notes (a description of the project, etc.).

Import Project Dialog

Importing Sequences

To analyze antibodies, you must import sequence data and optionally associate it with structural models (PDB files).

FASTA Format Requirements

Your FASTA file must contain the amino acid sequences for the Light and Heavy chains. Minimally the Fv, but full length sequences are recommended.

  • Split Chains: Identify Light and Heavy chains separately.
  • Matching Names: Use the same base name for both chains, appending _LC for Light Chains and _HC for Heavy Chains. This allows the system to automatically pair them into Fvs.

Example: 

>Ab001_LC
ESALTQPASVSGSPGQSITI...
>Ab001_HC
EVQLVQSGAEVKKPGASVKV...

PDB Association Logic

AbLead automatically associates optionally uploaded or built PDB files with your Fv sequences based on exact name matching.

  • Rule: If an Fv sequence has the basename Ab001, the system looks for Ab001.pdb in your uploaded files.
  • Effect: If a match is found, structural surface properties (SPH, SPP, SPN, SPCD) are calculated. If not, only sequence-based metrics are reported. The associated PDB file is also used in the Liabilities analysis.
  • Chain Labels: The PDB file should contain both chains, with the Light Chain labeled L and the Heavy Chain labeled H. This is required for the Liabilities analysis.

Run Analysis

Clicking Run Analysis will run the analysis on the project. Upon completion, the Project View may be displayed, or the dialog may be closed to return to the Dashboard.

Project Sharing

Projects can be shared with other users within the same organization (same email domain) on the system directly from the Project View. If you have the appropriate permissions, clicking Share will open a dialog allowing you to add users by email and define their access level: * Read-Only: Shared users can view all project data, run analyses that do not save data (like exporting or viewing variants), but they cannot save any modifications, apply mutations, or delete the project. * Write: Shared users have full modification permissions to edit, engineer, and apply mutations to the project. * Grant: Shared users can additionally share the project with others and manage their permissions.

Export/Import Project (.zip)

A Project may be exported to a .zip file by clicking File > Export Project. This will create a .zip file containing the project name, notes, and all sequences and PDB files associated with the project. An exported Project may be imported by clicking File > Import Project (.zip). This will open a dialog allowing you to select a .zip file to import. The project will be imported into the Dashboard of the current user. This feature allows for offline project sharing or storage.

Deleting and Restoring Projects

Clicking File > Delete Project will delete the project. Clicking File > Trash shows the Trash view. Here the trash may be emptied or project(s) restored to the Dashboard.

Labels

Labels are used to group and filter projects. Clicking Labels > New Label will open a dialog allowing you to create and nest new labels. Clicking Labels > Manage Labels will open a dialog allowing you to edit or delete existing label. Clicking Labels > Apply Label with selected Projects will apply or remove the selected labels to the selected projects.

Project Names and Notes

Double click empty space in project name field and or anywhere in a notes field to edit the project name or notes.

Logout

Clicking File > Logout will log you out of the application.