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.

Launch Web App  |  Documentation  |  Privacy Policy

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.

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Screenshots

Mobile (iPhone)

Tablet (iPad)

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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

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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

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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

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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   │
└──────────────────────────────────────┘

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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

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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

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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

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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)

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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

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Contact

For research inquiries, funding, and collaboration: [email protected]

License

MIT

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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.