DockIt

Features

Examples Gallery

MolDock includes 16 curated famous protein-ligand dockings across 7 categories. Search, filter, and tap any example to skip straight to docking with pre-filled protein and ligand.

Categories: Cancer, Antiviral, Neuroscience, Cardiovascular, Pain & Inflammation, Metabolic, Antibiotic

Docking Workflow

MolDock guides you through a 4-step molecular docking process:

Mobile App (iOS & Android)

MolDock includes a standalone Expo React Native mobile app in the mobile/ directory. It provides the same 4-step docking workflow, examples gallery, and results viewer — optimized for touch.

Running Locally

cd mobile
npm install
npx expo start

Scan the QR code with Expo Go on your phone, or press i for iOS simulator / a for Android emulator.

Building for App Store / Play Store

# Install EAS CLI
npm install -g eas-cli

# Configure (first time only)
eas build:configure

# Build for both platforms
eas build --platform all

# Submit to stores
eas submit --platform ios
eas submit --platform android

App Configuration

Quick Start

Prerequisites

• Node.js 18+
• Python 3.9+
• AutoDock Vina — vina binary in PATH
• Open Babel — obabel binary in PATH

Installation

# Clone the repository
git clone https://github.com/johnseong/LCBC-Dock.git
cd LCBC-Dock

# Install frontend dependencies
npm install

# Install backend dependencies
pip3 install -r requirements.txt

# Copy and configure environment variables
cp .env.example .env

Development

# Start both frontend and backend concurrently
npm run dev

# Or run separately:
npm run next-dev      # Frontend on :3000
npm run fastapi-dev   # Backend on :8000

Open http://localhost:3000 to access the app.

API Reference

The FastAPI backend exposes a RESTful API. Interactive docs are available at /docs when the backend is running.

Protein Endpoints

Ligand Endpoints

Docking Endpoints

POST /api/dock — Request Body

{
  "protein_pdb_id": "4HG7",
  "ligand_cid": 11314340,
  "ligand_name": "Nutlin-3a",
  "center_x": 0.0,        // auto-computed if all zeros
  "center_y": 0.0,
  "center_z": 0.0,
  "size_x": 20.0,         // grid box size in Angstroms
  "size_y": 20.0,
  "size_z": 20.0,
  "exhaustiveness": 8,     // 1-32, higher = more thorough
  "num_modes": 9,          // number of poses to generate
  "energy_range": 3.0,     // kcal/mol
  "email": "user@example.com"  // optional
}

Configuration

All configuration is through environment variables. Copy .env.example to .env and update:

Gmail Setup

To use Gmail for notifications:

1. Enable 2-Factor Authentication on your Google account
2. Generate an App Password
3. Set SMTP_USER to your Gmail address and SMTP_PASS to the app password

CapRover Deployment

MolDock uses two CapRover apps: lcbc-client (frontend, port 3000) and lcbc-server (backend, port 8000).

Prerequisites

• A CapRover server (e.g. captain.apps.yourdomain.com)
• CapRover CLI: npm install -g caprover
• Two apps in the dashboard: lcbc-client and lcbc-server

Deploy Script

The included deploy.sh handles the captain-definition swap automatically:

# Login to CapRover (one-time, saves credentials)
caprover login

# Deploy everything (frontend + backend)
bash deploy.sh all

# Deploy frontend only
bash deploy.sh frontend

# Deploy backend only
bash deploy.sh backend

CapRover App Setup

Backend Configuration

In CapRover dashboard → lcbc-server → App Configs:

Bulk Edit Environment Variables

Go to Environmental Variables → Bulk Edit and paste:

SMTP_USER=yourname@gmail.com
SMTP_PASS=your_16_char_app_password
FROM_EMAIL=yourname@gmail.com
BASE_URL=https://lcbc-client.apps.johnseong.com

Persistent Storage

Go to Persistent Directories and add:

This keeps the SQLite database alive across redeploys.

HTTPS

Go to HTTP Settings → Enable HTTPS for both apps.

Verify Deployment

# Check backend health
curl https://lcbc-server.apps.johnseong.com/
# Expected: {"message":"MolDock API v2.0 is running!","docs":"/docs"}

# Check frontend
open https://lcbc-client.apps.johnseong.com

# If backend returns 502, redeploy it
bash deploy.sh backend

Docker (Standalone)

The backend Docker image includes AutoDock Vina 1.2.5 and Open Babel pre-installed.

Backend

docker build -f Dockerfile.backend -t dockit-api .

docker run -p 8000:8000 \
  -e SMTP_USER=your@email.com \
  -e SMTP_PASS=your-app-password \
  -e BASE_URL=https://lcbc-client.apps.johnseong.com \
  -v lcbc-data:/app/data \
  dockit-api

The -v lcbc-data:/app/data flag persists the SQLite database across container restarts.

Frontend

docker build -f Dockerfile.frontend -t dockit-web .
docker run -p 3000:3000 dockit-web

Architecture

Docking Pipeline

When a job is submitted, the background worker:

1. Downloads the protein PDB from RCSB
2. Cleans the protein (removes water, heteroatoms)
3. Auto-computes grid center if not specified
4. Converts protein to PDBQT format (via Open Babel)
5. Downloads the ligand 3D SDF from PubChem
6. Converts ligand to PDBQT format
7. Runs AutoDock Vina with user-specified parameters
8. Parses output poses and binding affinities
9. Converts docked output to PDB for viewer
10. Stores results in database and sends email notification