AutoDock Vina

Classical molecular docking tool for drug discovery and high-throughput virtual screening. AutoDock Vina is the industry-standard docking platform with proven accuracy across thousands of protein-ligand complexes, offering dual scoring functions (fast empirical Vina scoring and detailed AutoDock4 physics-based analysis). Its parallel processing capabilities enable efficient screening of large compound libraries, as demonstrated in our GLP-1 receptor tutorial with 4,278 FDA compounds achieving 98.9% success rate, making it ideal for lead discovery and optimization campaigns.

Key Features

  • High-Throughput Screening: Efficiently screen large compound libraries
  • Dual Scoring Functions: Vina (fast) or AutoDock4 (detailed energy breakdown)
  • Validated Platform: Proven accuracy on thousands of protein-ligand complexes
  • Parallel Processing: Multi-threading for faster results

Input Requirements

Structure Preparation

  • Receptor: PDB file with proper preparation (hydrogens, charges)
  • Ligands: SDF, PDB, or MOL2 format with 3D coordinates
  • Search Box: Define binding site coordinates and dimensions

Key Parameters

  • Exhaustiveness: 8 (screening) to 32+ (detailed analysis)
  • Number of Poses: 5-9 output conformations
  • Energy Range: 3-5 kcal/mol difference threshold
  • Scoring Function: Vina (fast) or AutoDock4 (detailed)

Virtual Screening Example

Based on the GLP-1 receptor tutorial:

  • Target: GLP-1 receptor (PDB: 7S15)
  • Library: 4,278 FDA-approved compounds
  • Parameters: Exhaustiveness=8, 25Å×25Å×25Å search box
  • Results: 98.9% success rate with comprehensive binding analysis

Scoring Interpretation: < -10 kcal/mol (excellent), -10 to -8 (good), -8 to -6 (moderate), > -6 (weak binding)

Integration Workflows

  • Virtual screening → Docking Report → Binding analysis and hit classification
  • Structure preparation → AutoDock Vina → GROMACS validation
  • Boltz-2 prediction → AutoDock Vina screening

Tutorials