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
• Running ChemSTEP (Auto DOCK and Build)
  • 1. Source Environment
  • 2. Dock the Seed Set
  • 3. Gather Scores for the Seed Set
  • 4. Convert Scores to .npy Files
  • 5. Set Up the ChemSTEP Run Directory
  • 6. Edit params.txt
  • 7. Edit run_chemstep.py
  • 8. Launch the Job
  • 9. Monitor Job Status
  • 10. View Beacon SMILES and IDs
  • 11. Plot Hit Recovery
  • 12. Get Poses After Docking