CDD Vault Update (September #2 2025): Chemically Aware Antibody Registration

Compose Macromolecule Importer:

Compose Macromolecule mode now includes an “Antibody/ADC” option to compose your antibody and ADC molecules.

Antibody chains can be uploaded as linear amino acid sequences or as molecule IDs that reference pre-registered amino acid chains in your CDD Vault. The system supports monospecific antibodies as well as multispecific antibodies with the ability to map H1/H2 and/or L1/L2 chains.

For antibody drug conjugates (ADCs), linker/payload molecules can be marked via SMILES string, Molfile or CDD Vault ID with conjugation via H₂ or H₂O condensation. Registration supports up to 4 unique molecules for conjugation.

The chemistry underlying the amino acids is stored within CDD Vault, allowing for the seamless use of custom and unnatural amino acid monomers, as well as verification of site specific metadata compatibility. Cysteines are marked for disulfide bond formation, and amino acids marked for conjugation must have an available R-group for drug conjugation.

Antibody and ADC Rendering:

Users can append metadata to the end of an amino acid sequence to map domain locations of interest within the antibody chain, mark cysteine residues for disulfide bond formation and conjugation site amino acids for site directed conjugation. CDD Vault will automatically render antibodies and ADC images based on the sequences provided and available metadata.

By default, each chain contains a color-coded barcode, where each color represents a different amino acid type, allowing for visual comparisons between antibodies. If no metadata is provided, Vault will render a proto-Y shape, showing the color coded barcode but without the connection points. This rendering can be enriched with domain information, disulfide bond residues and conjugation sites.

ADC with No Metadata and Optional Drug Antibody Ratio (DAR)  > ADC with Disulfide Bonds, Domains and Conjugation Points

To provide feedback on features, or if you have questions and want to schedule a demo, please contact support@collaborativedrug.com.