September 29, 2025
Hello, CDD users!
Fall has arrived and so has the newest development in advanced macromolecule and bioconjugate registration in CDD Vault. Building off the success of macromolecule registration earlier this year, CDD Vault now includes a seamless method for registering chemically-aware antibodiesy and antibody drug conjugates (ADC). In contrast to other registration systems, chemically-aware biologics represent every atom connection precisely upon registration, enabling superior analyses and trend predictions. It simultaneously provides researchers the best of both sequence and atomistic views.
Layer 1 - Monomer chemistry
Using the same self contained sequence representation (SCSR) v3000 molfile registration introduced into CDD Vault earlier this year, we store antibody heavy and light chains as linear monomer sequences while fully capturing the underlying chemistry. This enables registration of chains containing unnatural, synthetic and custom amino acids for use in your antibodies and ADCs, for example with the rare trace amino acid seleno-cysteine 386 (or any other building block you can imagine):
Monomer chemistry views: Antibody chain with a seleno-cysteine monomer.
Layer 2 - Component based registration
The macromolecule composer within the import data wizard now includes an Antibody/ADC option. Within the composer, you can quickly map your heavy chain(s), light chain(s) and drug conjugate(s), easily supporting any 4-chained symmetric or multifunctional antibody. CDD Vault supports the creation of ADCs with anywhere from 1 (single payload ADC) to 4 (quad payload ADC) unique structures. The components are represented as a proto-Y shaped antibody with amino acid encoded color coded chains with explicit attachment points for structures, making it easy to visually compare sequence homology.
Component base registration: The macromolecule editor import data wizard maps your antibody chains (as a sequence or CDD Vault ID) and drug conjugates (as molfile, SMILES or CDD Vault ID).
Proto-Y shape molecule: Barcode view rendered after mapping antibody components.
Layer 3 - Biologic metadata
Enrich your registered antibody by indicating domain regions, disulfide bond residues, hinge region and drug conjugation sites. This information is used by CDD Vault to label your domains, and connect your antibody chains at the proper cysteine residue disulfide bonds. Additionally, drug conjugation sites are used to properly bind and visualize your linker-payload structures at the correct positions on the ADC.
Biologic metadata: Antibody (left) and ADC (right) renderings from chemically aware sequences.
Given CDD Vault’s flexible registration system, data can be stored at all 3 levels depending on what information you have available. Register your chain sequences with custom monomers (layer 1), register your antibody chains together in a single entity (layer 2) or supply additional metadata to fully annotate your antibody (level 3), all in a single system.
A wide variety of antibody and ADC modalities are supported, including bispecific antibodies and dual payload ADCs. Contact support@collaborativedrug.com, if there are additional modalities you’d like supported in the future. Create unique registration IDs, capture assay data and calculate curves for your antibodies and ADCs, all within the familiar integrated CDD Vault ecosystem. Keep track of your stock in the Inventory system, track your assay development with CDD Vault’s Assays and reference antibodies and ADCs in ELN to capture your experimental process with ease.
Precise capture of all information: Bispecific antibody (above) and a dual payload ADC (below) rendered in CDD Vault. Represent the exact format in nature with every atom captured on your computer.
CDD Support is always happy to schedule a working session to help you utilize these features in CDD Vault. Just email CDD Support to schedule your feature review!
If this Vault Snack leaves you hungry for more, all previous Vault Snacks can be found here and as always, feel free to contact CDD Support — we are available to help you succeed in using CDD Vault.