Dock Analysis

Universal docking result analyzer — HDOCK, HADDOCK 2.4, Vina, ClusPro output to reports, visualizations, and binding analysis.

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What's New in v2.0

• HADDOCK 2.4 support — parse HADDOCK output (score lists, cluster analysis)
• Multi-server comparison — analyze HDOCK and HADDOCK results side-by-side
• Enhanced cluster analysis — automatic clustering by score proximity
• H-bond detection — identify hydrogen bonds at protein-DNA interface

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Quick Start

# Analyze HDOCK results
python scripts/hdock_analyzer.py --input hdock_results.tar.gz --output analysis/

# Analyze HADDOCK results
python scripts/haddock_analyzer.py --input run1/ --output analysis/

# Compare multiple HADDOCK runs
python scripts/haddock_analyzer.py --input run1/ run2/ run3/ --output comparison/

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Analyzer Scripts

Script	Input	Server
hdock_analyzer.py	HDOCK tar.gz or extracted folder	HDOCK
haddock_analyzer.py	HADDOCK output directory	HADDOCK 2.4
compare_docks.py	Multiple docking results	Any

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What Each Script Does

hdock_analyzer.py — HDOCK Analysis

• Parses HDOCK .out score files
• Extracts interface contact files
• Generates binding residue frequency analysis
• Produces PyMOL visualization scripts
• Outputs Markdown + HTML reports

haddock_analyzer.py — HADDOCK Analysis

• Parses the_score.list files
• Analyzes individual model PDBs for contacts
• Automatic cluster detection (by score proximity)
• Decomposes HADDOCK score into components (vdW, elec, desolv, BSA)
• Generates PyMOL scripts with cluster visualization
• Outputs Markdown + HTML reports + JSON

compare_docks.py — Multi-Result Comparison

• Compare scores across different docking runs
• Identify common binding residues
• Generate comparative reports

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Output Files

HDOCK Analysis Output

analysis/
├── report.md                    # Markdown report
├── report.html                  # HTML report (open in browser)
├── hdock_analysis.json          # Machine-readable results
├── pymol_visualize.py           # PyMOL visualization script
└── binding_residues.csv         # Contact residue details

HADDOCK Analysis Output

analysis/
├── report.md                    # Markdown report
├── report.html                  # HTML report
├── haddock_analysis.json        # Machine-readable results
├── pymol_visualize.py           # PyMOL visualization script
└── binding_residues.csv         # Contact residue details

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HADDOCK Score Components

HADDOCK decomposes the total score into physically meaningful terms:

Component	Description	Weight
vdw	van der Waals interactions	0.1
elec	Electrostatic interactions	1.0
desolv	Desolvation energy	1.0
AIR	Ambiguous Interaction Restraints	0.01
BSA	Buried Surface Area	-0.005

Total HADDOCK score = 0.1×vdW + 1.0×elec + 1.0×desolv + 0.01×AIR − 0.005×BSA

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Usage Examples

Analyze HDOCK Tarball

python scripts/hdock_analyzer.py \
    --input results/hdock_job12345.tar.gz \
    --output analysis/hdock_job12345

Analyze HADDOCK Run

python scripts/haddock_analyzer.py \
    --input /path/to/haddock_run1/ \
    --output analysis/haddock_run1

Compare Multiple HADDOCK Runs

python scripts/haddock_analyzer.py \
    --input run1/ run2/ run3/ \
    --output comparison/

Generate Only HTML Report

python scripts/haddock_analyzer.py \
    --input run1/ \
    --output analysis/ \
    --format html

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PyMOL Visualization

After analysis, run the generated PyMOL script:

# View in PyMOL
pymol analysis/pymol_visualize.py

# Or from PyMOL GUI
File → Run Script → analysis/pymol_visualize.py

The script shows:

• Protein receptor (gray cartoon + surface)
• DNA/RNA ligand (orange sticks + phosphorus spheres)
• Binding site residues (yellow sticks)
• Hydrogen bonds (dashed lines)
• Top cluster models (colored by cluster)

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Installation

Prerequisites

• Python 3.9+
• Conda/Mamba

Setup

# Clone repository
git clone https://github.com/CliffVale/dock_analysis.git
cd dock_analysis

# Create environment
conda env create -f environment.yml
conda activate dock_analysis

# Verify
python scripts/hdock_analyzer.py --help
python scripts/haddock_analyzer.py --help

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Project Structure

dock_analysis/
├── README.md                    # This file
├── environment.yml              # Conda environment
├── scripts/
│   ├── hdock_analyzer.py        # HDOCK output parser
│   ├── haddock_analyzer.py      # HADDOCK output parser
│   └── compare_docks.py         # Multi-result comparison
├── data/                        # Sample data
├── results/                     # Example outputs
├── examples/                    # Usage examples
└── docs/
    └── TUTORIAL.md              # Step-by-step guide

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Citation

If you use this tool, please cite:

1. HDOCK: Yan et al. (2017) "HDOCK: a web server for protein-protein and protein-DNA/RNA docking" Nucleic Acids Research
2. HADDOCK: van Zundert et al. (2016) "The HADDOCK2.4 web server" Nucleic Acids Research

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License

MIT License

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Contributing

Contributions welcome! Please open an issue or PR.