Docking Analysis & Reporting

Comprehensive analysis and interactive visualization tools for evaluating molecular docking results from DiffDock, DiffDock-PP, and AutoDock Vina workflows. This advanced reporting system automatically processes docking outputs to generate publication-quality dashboards featuring CAPRI metrics for protein-protein interactions, binding affinity classification for virtual screening, statistical distributions, and interactive 3D visualizations. The platform provides detailed insights including confidence scoring, RMSD calculations, hit identification, chemical diversity assessment, and multi-method comparative analysis essential for making informed decisions in drug discovery pipelines.

Key Features

  • CAPRI Metrics: Industry-standard protein-protein docking evaluation
  • Interactive Dashboards: Web-based visualization with filtering and sorting
  • Comparative Analysis: Side-by-side comparison of different docking methods
  • Statistical Analysis: Score distributions, clustering, and outlier detection

Analysis Capabilities

Protein-Protein Docking (DiffDock-PP)

Confidence Score Classification

  • High Confidence: score > 0
  • Moderate Confidence: -1.5 < score ≤ 0
  • Low Confidence: score ≤ -1.5

RMSD Metrics (when reference available)

  • Complex RMSD: Overall complex structure accuracy
  • Ligand RMSD: Ligand protein placement accuracy
  • Interface RMSD: Binding interface accuracy

Additional Analysis

  • Pose Ranking: All 40 poses ranked by confidence
  • PDB Export: Top 5 poses exported for visualization
  • Filtering: Automatic removal of infinite confidence scores

Virtual Screening Dashboard (AutoDock Vina)

Summary Metrics

  • Total compounds: Complete library size and success rate
  • Best affinity: Strongest binding score identified
  • Hit classification: Automatic categorization by binding strength
  • Statistical analysis: Mean, median, and distribution metrics

Hit Classification

  • Excellent hits (< -10 kcal/mol): Strong binding candidates
  • Good hits (-10 to -8 kcal/mol): Moderate binding potential
  • Moderate hits (-8 to -6 kcal/mol): Weak binding interactions
  • Weak hits (≥ -6 kcal/mol): Poor binding affinity

Interactive Features

  • Affinity distribution plots: Histogram of binding scores
  • Top hits ranking: Best compounds with Z-scores
  • Enrichment analysis: Hit concentration assessment
  • Export options: Download data for further analysis

Interactive Dashboard Features

Real-Time Visualization

  • Summary Statistics: Pose distribution and top performers
  • Score Plots: Interactive histograms and scatter plots
  • 3D Gallery: Structure viewer with Mol* integration
  • Comparison Tools: Side-by-side pose evaluation

Customizable Reports

  • HTML Dashboard: Interactive plots with filtering and export
  • Statistical Reports: Distribution analysis and correlations
  • Data Tables: Sortable results with customizable columns
  • Structure Export: Annotated PDB/SDF files

Application Integration

DiffDock Processing

  • Automatic SDF output file processing
  • Confidence score extraction and ranking
  • RMSD calculation when references available
  • Interaction fingerprint generation

DiffDock-PP Processing

  • PDB pose file analysis
  • Full CAPRI metrics calculation
  • Interface property characterization
  • Complex quality assessment

AutoDock Vina Processing

  • PDBQT output parsing
  • Binding affinity extraction
  • Format conversion for analysis

Analysis Workflows

Standard Protein-Protein Analysis

  1. Input Processing: Load and validate docking results
  2. CAPRI Evaluation: Calculate I-RMSD, L-RMSD, FNAT
  3. Interface Analysis: Map contacts and interaction areas
  4. Report Generation: Create interactive dashboards

Virtual Screening Analysis

Hit Identification

  • Score-based ranking with statistical analysis
  • Chemical diversity assessment to avoid bias
  • Known active recovery for validation
  • False positive filtering using multiple criteria

Lead Optimization

  • Structure-activity relationships from poses
  • Binding mode clustering to identify series
  • Optimization suggestions based on interactions
  • Selectivity predictions against related targets

Integration Examples

Antibody-Antigen Analysis

DiffDock-PP → Docking Dashboard
- CAPRI metrics for all poses
- Interface hotspot identification
- Crystal structure comparison
- Binding energy decomposition

High-throughput Virtual Screening

AutoDock Vina → Virtual Screening Dashboard
- 4,278 compounds screened with 98.9% success rate
- Hit classification by binding affinity thresholds
- Statistical analysis with mean (-11.55 kcal/mol) and best (-23.12 kcal/mol)
- 69.7% excellent hits (< -10 kcal/mol) identified
- 6.5x enrichment factor in top compounds

Tutorials