The registration of peptides and proteins has become a default part of the CDD Vault registration process. When a peptide or protein sequence is added via the structure editing tool, it is automatically converted into a chemical structure (mol file format).
Background
Historically, peptides and proteins are being registered in CDD Vault using only amino acid sequences, especially when their complete chemical structures were unknown. This approach often led to inaccurate molecular weights due to the absence of linking bonds between monomers, limiting the reliability of structure-based computations.
With the introduction of the Macromolecule feature in CDD Vault, it is now possible to register peptides and proteins as fully defined chemical entities, preserving both their structural integrity and chemical properties.
CDD now generates a Self-Contained Sequence Representation (SCSR) using a V3000 mol file format for each entered or drawn sequence. This format provides several advantages:
- Self-contained: No external dictionaries are required.
- Scalable and reusable: Monomers are stored as reusable templates.
- 2D layout information: Includes a chemically meaningful sketch for visualization.
- Full atomic structure: Linking bonds are correctly implied, allowing accurate molecular weight calculations and chemical analysis.
- Sequence data embedded: Ideal for both cheminformatics and bioinformatics applications.
This advancement ensures that peptide and protein registrations in CDD Vault are robust, searchable, and chemically accurate, supporting a wide range of research and discovery workflows.
Registration Methods
A single peptide or protein can be registered:
- Along with or without salt/solvent.
- With associated batch and sample-level information.
- Through:
- The Explore Data tab:
Create a New… > Molecule - Or the Molecule page:
+ Create a New Molecule
- The Explore Data tab:
Steps to Register a Peptide or Protein
Launch the Structure Editor
- Click "Launch the Structure Editor" to open the editing tool.
Switch to Macromolecule Mode
- In the editor, switch to Macromolecules mode (top right corner).
- Click “PEP” to input the sequence manually, or use “Open Structure” to upload an existing structure.
Add Salt or Solvent Information (Optional)
To enter salt/solvent details textually (not embedded in the structure object):
- Select the Stoichiometry radio button.
- For Salts:
- Enter the ratio.
- Begin typing the salt name and choose from the filtered list.
- For Solvents:
- Enter the solvent ratio and select from the dropdown list.
Complete Molecule and Batch Information
- Fill out any relevant fields in the Molecule and Batch Information sections.
Assign to a Project
- Choose the appropriate Project from the list.
Create the Molecule
- Click the green “Create Molecule” button to complete registration.