CDD Vault Update (February #2 2025):  Advanced Macromolecules - Modified Bioconjugates Support in CDD Vault

Structure Editor Macromolecule Mode:

• CDD Vault now includes a Macromolecule mode for composing and editing DNA, RNA, and Peptide sequences, including support for unnatural modified bioconjugates.
• Macromolecule mode supports viewing sequences as letter codes or as components.
• Easily search and browse the expanding library of unnatural amino acids.
• Utilize the RNA builder to specify sugar, base, and phosphate modifications for custom nucleotides.
• Structures can be pasted or uploaded in IDT, HELM, or FASTA formats, or they can be drawn directly using Ketcher.
• Hover over monomers to view their underlying chemical structure or switch to molecule mode to expand monomers and see the full atomistic form.

Register Macromolecules:

• Single-entity registration can now be done through the Ketcher structure editor macromolecule mode.
• Bulk upload macromolecules using the new Compose Macromolecules option in the import data tab:
  • Supports the creation of linear peptides, cyclic peptides, and oligonucleotides such as double-stranded DNA or single-stranded RNA structures from strings in a CSV or XLSX file.
  • Use 1 letter codes, 3 letter codes, or custom codes within brackets.
  • Text-based sequences are converted to molfiles with self-contained sequence representation (SCSR) which are then mapped to structure.
  • Any metadata and protocol information is mapped per the usual mapping process, and all information is imported from a single file for both linear and cyclic entities.

View the Underlying Chemical Structure of Monomers From Macromolecules Registered in Vault:

• To view the chemical structure and attachment points of a monomer, first click to view the structure preview of a registered macromolecule, then hover over the monomer.
• The structure is automatically oriented according to the preview. 

We are committed to continuously improving the registration of modified bioconjugates in the upcoming quarters, guided by our growing community of subject matter experts. CDD Vault can now support one or multiple different entity types. We welcome your feedback and will be releasing new features regularly.

For assistance, questions, or to schedule a demo, please contact support@collaborativedrug.com.