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Assembler

Rebuild antibodies from their Fvs by selecting and dragging domain types such as Leader, KC, LC, CH1, Hinge, CH2, CH3-CHS, Linkers, and Multispecific parts.

This tool is useful for rebuilding antibodies from their Fvs in bulk or designing complex multi-chain formats, reducing human error and time.

The Assembler is a key implementation of the core work principle to "Be Inherently Lazy" (working very hard to build an easy, reproducible, and error-eliminating method to do work). Rather than manually copying, pasting, and concatenating variable regions and constant domains in Excel or text files to build formatted heavy and light chains—a tedious chore highly vulnerable to frame-shifts and copy-paste errors—you can use the Assembler to stitch domains together systematically and rebuild entire lead cohorts or multispecific configurations with drag-and-drop ease.

Accessing the Tool

Select at least one antibody in the Project View. Go to the Edit menu and select Assembler. This will open the Assembler workspace in a new tab.

Batch Mode

Batch Mode is designed for rebuilding standard monoclonal antibodies (mAbs) in bulk.

Assembler Batch Mode

  • Select Entries: The variable regions (VH and VL) from the selected entries populate the tool.
  • Select Domains: Expand a domain type from the sidebar, select the desired constant domain, and drag it to the appropriate row (Kappa Chain, Lambda Chain, or Heavy Chain) relative to the variable domains.
  • Apply to All: The dragged constant domains are applied to all selected entries in the batch, combining each entry's variable domains with the selected constant domains.
  • Build Options:
    • Build FASTA: Generates and downloads the assembled antibody sequences as a FASTA file.
    • Build New mAbs: Automatically processes and adds the assembled antibodies as new rows in the Project View grid.

Multispecific Mode

Multispecific Mode allows for the design of custom multi-chain structures, such as bispecifics, CrossMabs, scFvs, or fusion proteins.

Assembler Multispecific Mode

  • Custom Chains: Click + Add Chain to add an arbitrary number of chains to the construct.
  • Drag-and-Drop Assembly: Drag selected variable regions, native constant domains, linkers, or engineered parts into any chain row in any order.
  • Multispecific & Engineered Parts: The sidebar provides premium engineered parts for bispecific design, including:
    • Knobs-into-Holes (KiH): Stabilized Knob/Hole CH3 domains for IgG1 and IgG4.
    • CrossMab Crossover Parts: Swapped CH1-CL parts for Kappa and Lambda formats to ensure correct light chain pairing.
    • Linkers: Common flexible and rigid linkers.
  • User Custom Parts: Users can create their own custom sequences at the bottom of the sidebar. These parts persist per-user and can be dragged into any construct.
  • Parent Antibody: Users can designate a "Parent Antibody" from the project to track lineage and heritage.
  • Reconstruct and Re-edit: When opening the Assembler for an existing multispecific entry, the workspace automatically restores the exact layout, parts, names, and custom sequences.

Multispecific Entry Representation

Once built, a multispecific antibody is represented in the project view with multiple chains and placeholder scoring:

Multispecific Entry Representation

Multispecific Workflow

  1. In the Project View, select at least one entry
  2. Go to the Edit menu and select Assembler. This will open the Assembler workspace in a new tab.
  3. Click the Multispecific Mode tab.
  4. Click + Add Chain to add a new chain if needed.
  5. Drag and drop selected variable regions, native constant domains, linkers, or engineered parts into any chain row in any order.
  6. Set the Parent Antibody for lineage tracking.
  7. Click Build to generate the multispecific antibody as a new entry in the Project View.
  8. Use Extract Fvs to extract Fvs from an existing multispecific antibody.

[!NOTE] Multispecific Antibodies: Because multispecific antibodies consist of arbitrary multi-chain constructs (such as bispecifics or CrossMabs), they bypass sequence-level scoring and do not display residue-level stability, surface property, humanness, or liability analysis values in the Project View.

References

  • The Domain sequences were obtained using the IMGT/GENE-DB database.