Getting Started
Installation
- 1. Download the installer from novoquantnexus.com/novoworkbench
- 2. Open the DMG and drag NovoWorkbench to Applications
- 3. Launch NovoWorkbench — no Python, no dependencies required
System requirements: macOS 12+ (Apple Silicon & Intel). ~200MB disk space.
First launch
- 1. Click Open Folder to select a workspace directory containing your molecule files
- 2. NovoWorkbench indexes your files and displays them in the File Explorer
- 3. Click any molecule file to view its properties, 3D structure, and analysis
Your workspace is remembered between sessions and reopens automatically.
API key setup (optional)
Local features work immediately with no account. To unlock cloud-powered features (ADMET predictions, FAVES compliance, Ghost Molecule, Research Explorer), add your NovoMCP API key:
- 1. Open the Settings tab in the bottom panel
- 2. Paste your NovoMCP API key (nmcp_...) and click Save
- 3. Cloud features activate immediately
Workspace & Files
Supported file formats
| Format | Extension | Notes |
|---|---|---|
| SDF / SD | .sdf .sd | Multiple molecules per file |
| MOL | .mol | Single molecule with coordinates |
| PDB | .pdb | Protein and small molecule structures |
| SMILES | .smi | One SMILES string per line |
File Explorer
The left panel shows all molecule files in your workspace as a file tree. Click a file to load it into the editor, 3D viewer, and analysis panels. Multi-select files with Cmd-click (toggle) or Shift-click (range) for batch analysis.
Workspace indexing
When you open a workspace, NovoWorkbench indexes all molecule files in the background and computes molecular fingerprints. This enables instant similarity searching across your entire workspace.
Features
NovoWorkbench combines local compute with optional cloud intelligence. Local features run entirely on your machine; cloud features require a NovoMCP API key.
Local — always free, no account needed
Molecular Properties
Molecular weight, LogP, TPSA, hydrogen bond donors/acceptors, rotatable bonds, QED, synthetic accessibility score.
3D Visualization
Interactive 3D molecular viewer with ball-and-stick, surface, and licorice representations. Supports small molecules and proteins.
Druglikeness Rules
Five rule sets evaluated instantly: Lipinski Rule of Five, Veber, Ghose, Egan, and Muegge. Pass/fail indicators for each.
Structural Alerts
40+ PAINS pattern checks plus Lipinski violation detection. Alerts highlighted with severity indicators.
Similarity Search
Search your workspace for structurally similar compounds using Tanimoto similarity on Morgan and MACCS fingerprints.
Cloud-powered — requires NovoMCP API key
ADMET Predictions
40+ ML-based ADMET predictions with radar chart visualization, verdict badge (GO / CAUTION / NO-GO), and top risk summary.
FAVES Compliance
Full regulatory screening across DEA, FDA, CWC, EPA, and EU REACH. FAVES dimension scores, risk assessment, and regulatory pathway guidance.
Ghost Molecule
AI-generated molecular optimization suggestions. See Ghost Molecule section below.
Research Explorer
Search drug discovery literature, patents, bioRxiv preprints, ChEMBL bioactivity data, and clinical trials from within the desktop app.
Pipeline Orchestration
Bulk data workflows connecting external sources to NovoMCP processing. See Pipelines section below.
Credit Dashboard
Monitor your NovoMCP credit balance, per-tool usage breakdown, and overage alerts directly in the app.
Ghost Molecule
Ghost Molecule suggests optimized molecular variants while you work. When you paste or type a SMILES string, NovoWorkbench generates three optimization suggestions in the background:
- hERG — reduce cardiotoxicity risk
- Solubility — improve aqueous solubility
- Metabolic Stability — reduce first-pass metabolism
Controls
| Key | Action |
|---|---|
| Tab | Accept suggestion — replaces current SMILES and triggers re-analysis |
| Esc | Dismiss suggestion |
| ↑ / ↓ | Cycle through optimization targets |
Ghost Live Mode
Enable in Settings to get real-time suggestions as you edit SMILES. Disabled by default. When enabled, suggestions update automatically after a short pause in typing.
AI Chat
The right panel provides an AI chat interface for molecular analysis. Choose your preferred LLM provider in Settings:
| Provider | Authentication | Notes |
|---|---|---|
| Claude | Anthropic API key | Default provider |
| GPT | OpenAI API key | |
| Gemini | Google API key | |
| Ollama | None (local) | Fully offline — no data leaves your machine |
Built-in tools
The AI can invoke 5 chemistry tools during conversation:
Batch Analysis
- 1. Select 2 or more files in the File Explorer (Cmd-click or Shift-click)
- 2. Click the Analyze button in the Explorer header
- 3. Processing runs in the background with a progress indicator
- 4. Results appear in the Batch tab — properties, ADMET verdicts, and compliance status
- 5. Click Download to export results as CSV
Past batch runs are saved and accessible via the history button.
Pipelines
The Pipelines tab orchestrates bulk data workflows that pull compounds from external sources, process them through NovoMCP, and push enriched results back.
- 1. Select source — choose a connected data warehouse
- 2. Preview data — view table schema, row count, auto-detected SMILES column
- 3. Choose processing — toggle Properties, ADMET, Compliance, Optimize
- 4. Select destination — choose where to push and write mode
- 5. Review cost — credit estimate and confirmation
- 6. Run — live progress bar and log viewer
- 7. Results — status summary with job details
Keyboard Shortcuts
| Shortcut | Action | Context |
|---|---|---|
| Tab | Accept Ghost Molecule suggestion | Ghost overlay visible |
| Esc | Dismiss Ghost Molecule suggestion | Ghost overlay visible |
| ↑ / ↓ | Cycle optimization targets | Ghost overlay visible |
| Enter | Send chat message | Chat input focused |
| Shift + Enter | New line in chat | Chat input focused |
| Cmd-click | Toggle file selection | File Explorer |
| Shift-click | Range-select files | File Explorer |