Fragmenstein Web UI
March 30, 2026 · View on GitHub
A browser-based interface for the Fragmenstein.
Quick Start
cd web
./start.sh
Then open http://localhost:3000 in your browser.
The script will:
- Check that Python and Node.js are installed
- Install any missing dependencies automatically
- Start the backend (port 8000) and frontend (port 3000)
Press Ctrl+C to stop.
What You Can Do
- Upload a template protein (PDB) and hit fragment molecules (SDF/MOL/PDB)
- Combine fragments into new ligand candidates (pairwise merging)
- Find analogs via SmallWorld, PubChem, paste SMILES, or upload a compound library (CSV/Excel)
- Place analogs into the protein binding site
- Browse results with interactive 3D visualization, outcome charts, and CSV/SDF export
Requirements
- Python 3.10+ with Fragmenstein installed
- Node.js 18+
- PyRosetta (optional, for full energy scoring — without it, use Wictor mode)
Configuration
| Environment Variable | Default | Description |
|---|---|---|
BACKEND_PORT | 8000 | Backend API port |
FRONTEND_PORT | 3000 | Frontend UI port |
FRAG_DATA_DIR | ./data | Data storage directory |
CHEMSPACE_API_KEY | — | Optional. Enables ChemSpace analog search |
MOLPORT_API_KEY | — | Optional. Enables MolPort analog search |