Chemistry Data Management

Name: Scientific Activity Tracking Software
Author: CDD

Centralize chemical design, synthesis, bioactivity, and analytical data.

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Registration that thinks like a chemist.

Every structure registered accurately and every duplicate caught.

Every compound registered once. Salts and solvents stripped, structures standardized, and duplicates caught across every project and within each upload.
Stereochemistry as intended. V3000 enhanced stereo AND/OR labels register racemates, unknown pure enantiomers, and known enantiomers as separate molecules.
Atropisomers as distinct compounds. Axial chirality and other non‑tetrahedral cases are supported.
Tautomers flagged. When a possible tautomer is detected, the chemist decides: new batch, new molecule, or duplicate.
Register whole libraries in one import. Map data to custom fields, review a row‑by‑row QC report, and get IDs and properties generated automatically.

CDD Vault Registration

Tautomer recognition for bulk structure imports into CDD Vault

Every result connected to the batch that produced it.

The single source of truth from plate matrix data to endpoint values.

Create AI-ready datasets. Standardize data structure across computational, in vitro, and in vivo studies.
Rapidly identify hits. Intuitive search interface and customizable dashboards for high throughput analysis.
Advanced data analysis. Automate data processing, QC workflows, curve fitting, and custom calculations including IC50, MIC, Ki/Kd, Z/Z', PK/PD, and ADMET.
Ensure reproducibility and interoperability. Customizable assay annotation fields and built-in ontology templates provide context for AI/ML workflows.

CDD Vault Activity CDD Vault Curves

CDD Vault provides a comprehensive interface to review all data associated to a particular compound.

From reaction to registered compound in one interface.

Your electronic lab notebook, compound registry, and inventory stay in sync automatically.

Register from the stoichiometry table. Draw or import a reaction, then register products and reagents from the entry.
Automated stoichiometry calculations. Enter mass, moles, volume or density, and yield and expected mass update in real time.
Every batch and sample links to its experiment. ELN links are added to each record automatically.
Reagent stock debits from the ELN. Log what you used and your inventory updates.
Every sample located. Nested locations from building to freezer, rack and box, with printable barcodes.

CDD Vault Electronic Lab Notebook CDD Vault Inventory

stoichioimetry table for chemical reaction capture in CDD Vault

See the patterns in your data instantly.

Interactive plots and SAR tools built by chemists, for chemists.

R‑group decomposition. Pick a suggested core or draw your own, and plot R1 and R2 against any other experimental parameter.
Clustering and SuperSAR. Group molecules by Tanimoto similarity and filter by suggested SAR fragments.
A data table built for SAR. Color‑coded columns, on‑the‑fly calculations, custom MPO scores, and one‑click pivots.
2D and 3D plots. Generate multiparameter publication quality graphics through an intuitive interface.

CDD Vault Visualization

Explore new chemistry without exposing yours.

Generate virtual analogs, predict properties and activity, and check novelty securely in your CDD Vault.

Bioisostere suggestions. Explore new hypotheses by iteratively generating synthetically accessible compounds.
Predict ADMET before you synthesize. Use Lilly TuneLab to predict small-molecule ADMET properties across 33 common endpoints.
QSAR grounded in your own results. AI models build and retrain themselves from your assay data with nothing to configure and nothing to maintain.
Similarity search beyond your Vault. Search 41.2 million structures from ChEMBL, SureChEMBL, CDD Public, Enamine, and Enamine RealDiversity.
Fold and dock without sending structures anywhere.
Run Boltz2, AlphaFold2, ESMFold, and DiffDock on CDD’s managed infrastructure, with results stored beside your assay data.

CDD Vault AI Lilly TuneLab @ CDD Vault

Co-folding and docking use Boltz-2 in CDD Vault

Collaboration that doesn’t cost you your IP.

Outsource synthesis and screening without handing over your library. Partners work in one firewalled project; your team gets every result in one place.

Partners deliver AI-ready data instead of spreadsheets. CROs register compounds and upload results directly into your Vault, so nothing arrives as an email attachment or a slide deck.
Project-level permissions.
Access is granted one project at a time. A CRO working on a single series never sees the rest of your library.
Your team works across all data. External results sit beside your own data for SAR, analysis, and project tracking the moment they land.
Know where every external result came from. Audit trails record who registered or changed each record, so a CRO’s data is traceable years later.

Secure project management in CDD Vault allows for collaboration without exposing intellectual property (IP)

CDD Vault chemistry FAQ

How does CDD Vault handle salts and solvates when registering a compound?

CDD Vault strips salts and solvents from a drawn structure and records them on the batch, so the parent compound registers once. You can also enter salt and solvent information as stoichiometry instead of drawing it, choosing the ratio and selecting from a managed salt list.

Can CDD Vault register stereoisomers and atropisomers as separate compounds?

CDD Vault registers stereoisomers as drawn and uses V3000 enhanced stereochemistry AND and OR labels to distinguish a racemate, a pure enantiomer of unknown absolute configuration and a pure enantiomer of known configuration as separate molecules. Atropisomers and other non-tetrahedral chirality are supported.

How does CDD Vault detect duplicate compounds and tautomers?

CDD Vault checks uniqueness across the entire Vault and within each import file, using RDKit fingerprints with additional layers for isomer recognition. When a possible tautomer is detected, the chemist decides whether to register a new batch of the existing molecule or a new molecule entirely.

Can CDD Vault register mixtures and formulations?

The CDD Vault Mixture Editor registers mixtures and formulations with every component captured as its own chemical structure, amount and hierarchy. You can type a mixture name such as “ethanol (95%) in water” and have it parsed into components automatically, or compose many mixtures at once from spreadsheet columns during import.

What types of chemical structure search does CDD Vault support?

CDD Vault supports substructure search, exact structure search and Tanimoto similarity search. Each can be combined with searches over assay results, calculated properties, batch fields and collections, so a single query can return compounds matching both a structural motif and an activity threshold.

Do CDD Vault’s AI tools send my chemical structures to external services?

CDD Vault’s AI similarity search and bioisostere suggestions run inside the same secure computing environment as the rest of the platform. Your chemical structures are never sent to third-party AI services and are never used to train external models.

How do CROs contribute data in CDD Vault without seeing internal compounds?

Vault Administrators grant users access into select projects. A CRO registers compounds and uploads results into the project you share with them, and sees nothing outside it, while your internal team works across every project at once.

What file formats can I import compounds and assay data from?

CDD Vault imports compounds and assay data from CSV, Excel and SD files. The import wizard maps any column to any field, shows a row-by-row QC report before anything commits, and generates registration IDs and calculated properties automatically.

How does CDD Vault handle data provenance and audit trails?

CDD Vault records who registered or changed each record and when, so every record in the Vault stays traceable to the person and the project behind it. Externally sourced data from a CRO remains attributable long after the engagement ends.

Get started with CDD Vault for Chemistry

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