Skip to content

README.md

Latest commit

 

History

History
48 lines (33 loc) · 1.48 KB

README.md

File metadata and controls

48 lines (33 loc) · 1.48 KB
Raw

Fragmenstein Web UI

A browser-based interface for the Fragmenstein.

Sessions Page

Combine Page

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

  1. Upload a template protein (PDB) and hit fragment molecules (SDF/MOL/PDB)
  2. Combine fragments into new ligand candidates (pairwise merging)
  3. Find analogs via SmallWorld, PubChem, paste SMILES, or upload a compound library (CSV/Excel)
  4. Place analogs into the protein binding site
  5. 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