June 25, 2026
Automated antibody markup
When composing antibodies from the Import Data tab, a new checkbox triggers an algorithm that identifies the disulfide linkages between the Light and Heavy chains and tags the variable and constant regions on both chain types automatically. This first, deliberately conservative version works on antibodies that closely follow the standard pattern and will simply decline rather than risk making a bad call on anything unusual. Predicting disulfides and regions means imported sequences get the same high-level antibody markup as sequences that arrive fully decorated with metadata, which isn't always conveniently at hand. The screenshot below shows the same sequences imported with and without metadata assigned. The first row of the sequence highlights the newly added metadata.
Display custom monomers
Representing custom monomers accurately is critical for unnatural monomers, as well as all post-translational modifications (sugars, methyl groups, phosphates, etc). For example, if you want to accurately represent phosphotyrosine (pTyr), which plays a critical function in protein regulation, protein-protein interactions and signal transduction, you can now view the atomistic monomer details conveniently in your search result table. 
To view custom monomers, simply select the Monomer field in the “Customize Your Report” interface to display the monomer information associated with a registered molecule. The resulting monomer will have the desired connection points and properties for your structure-function analyses, such as MW for mass spectrometry (Mass Spec).
Display Mixture components:
Use the “Customize Your Report” link in a search table, and toggle the Mixture Components field to view the individual components alongside a registered Mixture.
Transpose data via the Import Data Parser:
The Import Data Parser reformats data into a “Tabular” data format: the correct format for uploading data to CDD Vault. Now, that reformatting includes transforming (pivoting) rows of data into columns. Simply select the rows, without the row headers, and select the “Rows” button on the right hand side of the parser. On the “Preview Import Table” tab, the rows display as columns with the row headers as the column headers.
Visualization Updates
Launch Visualization from the Explore Data tab:
Many new features have been released to Visualization to enhance the data table viewing experience, making it the place for searching, data analysis, plotting and SAR without the need for the search page. Create a search query and launch the results directly to a visualization table that mirrors the familiar search result table. For more information on the new Visualization updates you can check our past release notes or the recording from the Q2 Quarterly Product Update Webinar.
Copy and export a list of IDs:
Bulk copy unique Molecule and Batch identifiers such as Molecule IDs or Molecule-Batch IDs from a Visualization table. Only IDs of compounds selected in the table will be copied. Copying the IDs respects the sorting order.
Freeze columns in the data table:
Open the Visualization table settings by clicking on the gear icon in the top right hand corner. Lock/freeze a column of interest for scrolling by clicking the lock icon next to the field or dragging and dropping the field name above the grey horizontal line on the “Parameters” tab.
API Updates
Protocol and collection searches via the API:
GET Saved Searches - now returns all of the query parameters from a saved search including protocol and collection criterion.
Molecule(s) [GET, POST, PUT] - GET now accepts structure, collection, and protocol criteria allowing users to have more granular control over lists of returned Molecule IDs.
Batch(es) [GET, POST, PUT] - GET now accepts structure, collection, and protocol criteria allowing users to have more granular control over lists of returned Batch IDs.
These endpoints allow users to create more queries on the fly, rather than relying solely on saved searches.
API endpoints for Deep Learning Bioisosteric suggestions and Similarity searches:
You can now access Deep Learning Bioisosteric suggestions and Deep Learning Similarity searches from the AI module using the API. This allows you to integrate this functionality in your computational chemistry and design workflows.
Deep Learning Similarity
POST /api/v1/vaults/{vault_id}/ai/similarity
Submit a chemical structure and receive a ranked list of similar structures using the Deep Learning similarity model.
Bioisosteric replacements (hierarchical)
POST /api/v1/vaults/{vault_id}/ai/bioisosteres
Submit a chemical structure and receive bioisosteric replacement suggestions grouped by fragment.
Using these endpoints will require the AI module to be enabled in your Vault. Please contact support@collaborativedrug.com if you would like to enable this module. For more details, see our knowledge base article on the topic here.
To provide feedback on features, or if you have questions and want to schedule a demo, please contact support@collaborativedrug.com.