Demo: Molecular Docking
Docking Workflow

Ligand-X Demo

Demo: Molecular Docking

See Ligand-X performing high-throughput molecular docking with AutoDock Vina to predict ligand binding poses and affinities.

Video Walkthrough

Coming Soon: Video walkthrough demonstrating molecular docking in Ligand-X.

Data Flow Pipeline

When you submit a docking job, your data flows through these stages:

1. Receptor Preparation
  • Parse PDB structure
  • Remove waters/ions (optional)
  • Add polar hydrogens
  • Convert to PDBQT format (Meeko)
2. Ligand Preparation
  • Parse SDF/MOL/SMILES
  • Add hydrogens, generate 3D if needed
  • Assign Gasteiger charges
  • Detect rotatable bonds
  • Convert to PDBQT format
3. Grid Box Definition
  • Define search space in binding site
  • Center coordinates (x, y, z)
  • Box dimensions (default: 20×20×20 Å)
4. Docking Execution
  • AutoDock Vina search algorithm
  • Explore conformational space
  • Score poses with Vina scoring function
  • Generate ranked pose library
5. Pose Conversion
  • Convert PDBQT → SDF (preserves bonds)
  • Convert PDBQT → PDB (for MolStar)
Results
  • Ranked poses with relative binding scores
  • 3D visualization of each pose (MolStar)
  • RMSD values between poses
  • Download options (PDB, SDF, PDBQT)

Tools Used

Stage Tool Purpose
Receptor Prep Meeko Modern PDBQT preparation
Ligand Prep RDKit Molecule parsing, 3D generation
Format Conversion OpenBabel, Meeko PDBQT ↔ SDF/PDB
Docking AutoDock Vina Pose prediction and scoring
Visualization MolStar Interactive 3D viewer

Docking Parameters

Parameter Default Description
exhaustiveness 32 Search thoroughness (higher = slower, better)
num_modes 10 Maximum poses to return
energy_range 100.0 Energy range for poses (kcal/mol)
scoring vina Scoring function (vina, ad4, vinardo)

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