Advanced Uses

This section covers advanced docking setups.

• Warp Drives: Expanding the Reach of LSD
  • Retrieval Augmented Docking with Hierarchical Navigable Small Worlds
  • CHEM Step
  • Synthon-based Methods
• SymDOCK: Docking with Symmetry and Cooperativity
  • 1. What You Will Need
  • 2. Background Math
  • 3. Getting the Affine Transformation Matrix
  • 4. Extending the Protein Fibril and Ligand Stack
  • 5. Preparing for Blastermaster
  • 6. Modifying the INDOCK and Creating the affine_transformation.txt
  • 7. Generating and Modifiying the DOCK Score Grids
  • 8. Analyzing Results with Symmetry
• Covalent docking
  • Covalent docking