MolDock
Drug Discovery, On the Go. Powered by AutoDock Vina.
MolDock is a molecular docking platform that brings AutoDock Vina to your browser and phone. Search proteins and ligands from public databases, submit docking jobs, and visualize results — no installation required.
Available on Web, iOS, and Android.
Developed by John Wonmo Seong at University of California, Irvine in collaboration with Seoul National University. Special thanks to Professor Juyong Lee at the Computational Drug Discovery Lab.
Screenshots
Mobile (iPhone)
Tablet (iPad)
Features
- Protein Search — 200,000+ structures from RCSB PDB
- Ligand Search — 100M+ compounds from PubChem with 2D structures, formula, weight, and SMILES
- Protein Preparation — Removes water and heteroatoms, protonation at pH 7.4
- AutoDock Vina — Configurable exhaustiveness, auto-computed grid center
- Live Progress — Step-by-step status updates with ETA countdown and full log history
- 3D Viewer — Interactive 3Dmol.js viewer with cartoon/stick/surface modes and docked ligand overlay
- Examples Gallery — 16 famous dockings (Imatinib, Aspirin, Caffeine, Remdesivir, etc.) with search and category filters
- Email Notifications — Get notified when jobs complete or fail
- Download Results — Export docked poses in PDB or PDBQT format
- Mobile App — Native iOS & Android app with tablet-optimized layouts
- Live Stats — Queue length, completed jobs, and estimated wait time on the homepage
For researchers (v3)
- Virtual screening (
/screen) — paste SMILES or upload an SDF library, dock every ligand against one target, ranked table (affinity, ligand efficiency, H-bonds, key residues) + CSV export
- Protein prep — PDB ID or UniProt accession (AlphaFold DB model), chain selection, waters/hetero groups removed (metals optionally kept), hydrogens for a chosen pH + Gasteiger charges
- Binding site — co-crystallised ligand, residue list, automatic pocket detection (grid buriedness), or whole protein
- Redocking validation — heavy-atom RMSD of every pose to the crystal ligand (1HSG/indinavir: 0.57 Å)
- Interaction analysis — H-bonds, hydrophobic contacts, π-stacking, salt bridges, metal contacts; 2D interaction map + residue table per pose
- Reproducibility — recorded Vina/Open Babel/RDKit versions, seed, box, protonation, exact Vina command; methods paragraph and BibTeX
- Exports — poses SDF/PDBQT/PDB, complex PDB, PyMOL
.pml, ChimeraX .cxc, CSVs, params.json, or everything as one ZIP
- REST API —
X-API-Key: mdk_... (Pro). OpenAPI docs at /docs on the API server
Plans
| Free | Pro ($9.99/mo or $79/yr) | Lab / Institution (quote) |
|---|
| Dockings/day | 5 (3 without account) | 300, priority queue | 1000 per seat |
| Exhaustiveness / poses / box | 8 / 9 / 30 Å | 32 / 20 / 40 Å | 64 / 20 / 60 Å |
| Batch screening | 5 ligands | 500 per batch | 2000 per batch |
| Private jobs, API keys, kept forever | – | ✓ | ✓ |
Limits are enforced server-side (api/plans.py, api/accounts.py). Stripe price IDs come from the environment; see .env.example.
Tests
pip install -r requirements.txt pytest && pytest tests # needs Open Babel for the interaction tests
Examples Gallery
16 curated famous protein-ligand dockings across 7 categories. Tap any example to start docking instantly.
| Ligand | Protein | Category |
|---|
| Imatinib | BCR-ABL Kinase (1IEP) | Cancer |
| Nutlin-3a | MDM2 (4HG7) | Cancer |
| Aspirin | COX-2 (5IKR) | Pain & Inflammation |
| Caffeine | Adenosine A2A (3RFM) | Neuroscience |
| Sildenafil | PDE5 (1UDT) | Cardiovascular |
| Oseltamivir | Neuraminidase (2HT8) | Antiviral |
| Remdesivir | RdRp (7BV2) | Antiviral |
| Lopinavir | HIV-1 Protease (1MUI) | Antiviral |
| Paclitaxel | Tubulin (1JFF) | Cancer |
| Metformin | AMPK (4CFF) | Metabolic |
| Tamoxifen | Estrogen Receptor α (3ERT) | Cancer |
| Donepezil | Acetylcholinesterase (2RG6) | Neuroscience |
| Erlotinib | EGFR Kinase (3NYA) | Cancer |
| Atorvastatin | HMG-CoA Reductase (3OGP) | Cardiovascular |
| Methotrexate | DHFR (2ITO) | Cancer |
| Penicillin G | PBP (1PWC) | Antibiotic |
Docking Workflow
| Step | Page | Description |
|---|
| 1 | /docking/protein | Search and select a protein from RCSB PDB |
| 2 | /docking/marinate | Prepare protein (remove water, heteroatoms, add charges) |
| 3 | /docking/ligand | Search and select a ligand from PubChem |
| 4 | /docking/cook | Configure exhaustiveness, add email, and submit |
| — | /dashboard | Track job status with live progress and ETA |
| — | /examples | Browse 16 curated famous dockings |
| — | /results/[jobId] | 3D viewer with docked ligand, binding affinities, downloads |
Architecture
┌──────────────────────────────────────┐
│ Frontend (Next.js on CapRover) │
│ lcbc-client app │
│ │
│ /api/rcsb → RCSB PDB search │
│ /api/pubchem → PubChem search │
│ (server-side proxies, no CORS) │
│ │
│ /docking/* → protein/ligand flow │
│ /examples → curated docking gallery│
│ /dashboard → job tracking │
│ /results/* → 3D viewer + download │
└──────────────┬───────────────────────┘
│
│ POST /api/dock
│ GET /api/jobs/{id}
│ GET /api/results/{id}
▼
┌──────────────────────────────────────┐
│ Backend (FastAPI on CapRover) │
│ lcbc-server app │
│ │
│ ┌────────────────────────────────┐ │
│ │ Docking Worker Thread │ │
│ │ AutoDock Vina + Open Babel │ │
│ └────────────────────────────────┘ │
│ │
│ SQLite (/app/data/lcbc_dock.db) │
│ SMTP email notifications │
└──────────────────────────────────────┘
┌──────────────────────────────────────┐
│ Mobile App (Expo React Native) │
│ iOS & Android │
│ │
│ Same 4-step docking workflow │
│ Examples gallery with search │
│ 3Dmol.js viewer via WebView │
│ Direct API calls (no CORS proxy) │
│ Tablet-optimized responsive layout │
└──────────────────────────────────────┘
Project Structure
LCBC-Dock/
├── app/ # Next.js frontend (App Router)
│ ├── api/
│ │ ├── pubchem/route.ts # Server-side PubChem proxy
│ │ └── rcsb/route.ts # Server-side RCSB PDB proxy
│ ├── components/
│ │ └── ProteinViewer.tsx # 3Dmol.js interactive viewer
│ ├── docking/
│ │ ├── protein/page.tsx # Step 1: Protein search + 3D viewer
│ │ ├── marinate/page.tsx # Step 2: Protein preparation
│ │ ├── ligand/page.tsx # Step 3: Ligand search
│ │ └── cook/page.tsx # Step 4: Docking config + submit
│ ├── examples/page.tsx # Curated examples gallery
│ ├── dashboard/page.tsx # Job tracking with live progress
│ ├── results/[jobId]/page.tsx # Results + 3D docked pose viewer
│ ├── about/page.tsx
│ ├── layout.tsx
│ ├── page.tsx # Homepage with inline examples + stats
│ └── globals.css
├── mobile/ # Expo React Native app (iOS & Android)
│ ├── app/ # Expo Router screens
│ ├── components/ # ProteinViewer, StepIndicator, Spinner
│ ├── lib/ # API helpers, useLayout hook
│ ├── plugins/ # Kotlin version config plugin
│ ├── assets/ # App icons & splash screen
│ └── app.json # Expo config (iOS + Android)
├── api/ # FastAPI backend
│ ├── index.py # API endpoints + stats
│ ├── docking.py # Vina docking engine
│ ├── worker.py # Background job processor with progress
│ ├── database.py # SQLite + status message logging
│ ├── email_service.py # SMTP notifications
│ └── models.py # Pydantic models
├── screenshots/ # App Store screenshots
│ ├── *.PNG # iPhone (1284x2778)
│ └── ipad/*.PNG # iPad (2732x2048)
├── docs/ # GitHub Pages
│ ├── index.html # Documentation site
│ └── privacy.html # Privacy policy
├── Dockerfile.frontend
├── Dockerfile.backend
├── deploy.sh # CapRover deploy script
├── package.json
├── requirements.txt
└── README.md
Deployment
CapRover (Web)
# Login (one-time)
caprover login
# Deploy everything
bash deploy.sh all
# Deploy frontend or backend only
bash deploy.sh frontend
bash deploy.sh backend
| App | Dockerfile | Port |
|---|
lcbc-client | Dockerfile.frontend | 3000 |
lcbc-server | Dockerfile.backend | 8000 |
Backend Environment Variables
In CapRover dashboard → lcbc-server → Bulk Edit:
[email protected]
SMTP_PASS=your_16_char_app_password
[email protected]
BASE_URL=https://lcbc-client.apps.johnseong.com
Persistent storage: /app/data → lcbc-data
Mobile (App Store / Play Store)
cd mobile
npm install
eas build --platform all
eas submit --platform ios
eas submit --platform android
| Field | iOS | Android |
|---|
| Bundle ID | com.johnseong.dock-it | com.johnseong.dock_it |
| Backend | https://lcbc-server.apps.johnseong.com | same |
Local Development
git clone https://github.com/wonmor/LCBC-Dock.git
cd LCBC-Dock
npm install # Frontend
pip3 install -r requirements.txt # Backend
cp .env.example .env
npm run dev # Starts both on :3000 and :8000
Mobile
cd mobile
npm install
npx expo start
Tech Stack
| Layer | Technology |
|---|
| Web Frontend | Next.js 13, React 18, TypeScript, Tailwind CSS, 3Dmol.js |
| Mobile App | Expo SDK 52, React Native, Expo Router, WebView |
| Backend | FastAPI, Python 3.11, AutoDock Vina 1.2.5, Open Babel |
| Database | SQLite |
| Data Sources | RCSB Protein Data Bank, PubChem |
| Deployment | CapRover (web), EAS Build (mobile) |
| Email | SMTP (Gmail compatible) |
API Endpoints
| Method | Endpoint | Description |
|---|
GET | / | Health check |
GET | /api/stats | Queue stats (total, completed, wait time) |
GET | /api/proteins/search?q= | Search RCSB PDB |
GET | /api/proteins/{pdb_id} | Protein details |
GET | /api/proteins/{pdb_id}/center | Compute grid center |
GET | /api/ligands/search?q= | Search PubChem |
GET | /api/ligands/{cid} | Ligand details |
POST | /api/dock | Submit docking job |
GET | /api/jobs/{job_id} | Job status + progress message |
GET | /api/results/{job_id} | Docking results with poses |
GET | /api/results/{job_id}/download/pdb | Download PDB |
GET | /api/results/{job_id}/download/pdbqt | Download PDBQT |
Contact
For research inquiries, funding, and collaboration: [email protected]
License
MIT
Built by John Wonmo Seong at University of California, Irvine in collaboration with Seoul National University.
Special thanks to Professor Juyong Lee at the Computational Drug Discovery Lab.
