• Theory
  • Brief Definitions
  • Asymmetric Unit
  • Biological Unit
  • Biological Design Unit (BioDU)
  • Design Unit
  • Spruce TK Preparation Workflow
  • Proton Placement and Optimization
  • Protein Side Chain Modeling
  • Protein Loop Modeling
  • Protein Superposition
  • How to Correctly Read a PDB File
• Iridium
  • Categorization
• Simple Macromolecular Preparation Workflow
• Advanced Macromolecular Preparation Workflow
  • Inputs
  • Filtering and Standardization
  • Generating the Biological Unit
  • Generating Packing Residues
  • Enumerating Alternate Locations
  • Componentizing the System
  • Building Missing Pieces
  • Optimizing the Hydrogen Bond Network
  • Assignment on Radii and Partial Charges
  • Prepared Biological Units (BioDUs)
  • Enumerating Sites / Pockets
  • Assigning an Iridium Category
  • Generating a Docking Receptor
  • Superposition to a Common Frame of Reference