Tutorials

These tutorials cover the use of meeko in integration with other packages, including vina, autodock-gpu, ringtail, and molscrub.

Tutorials

• Basic Docking
  • Prerequisites and Environment Setup
  • Ligand Preparation
  • Receptor Preparation
  • Export Poses from Docking
• Reactive Docking
  • Introduction
  • Prerequisites and Environment Setup
  • Ligand Preparation
  • Receptor Preparation
  • Docking Calculation
  • Export the Docking Poses
• Tethered Docking
  • Introduction
  • Prerequisites and Environment Setup
  • Ligand Conformer Generation
  • Receptor Preparation
  • Covalent Ligand Preparation
  • Docking Calculation
  • Export the Docking Poses
• Preparation and Execution of Virtual Screening with AutoDock-GPU
  • Introduction
  • Ligand Preparation
  • Receptor Preparation
  • Execution of Docking Calculations
• Retrospective Docking Analysis and Model Building
  • Introduction
  • Additional Dependencies
  • Single-Pose Molecule Reconstruction
  • Basic Metrics (ROC AUC, EF) based on Single Numerical Metric
  • Vectorization of Interactions
  • Logistic Regression and Explanation by Coefficients
  • XGBoost Modeling and Explanation with SHAP
• Anchored Docking
  • 1. Receptor preparation
  • 2. Ligand preparation
  • 3. Run autogrid
  • 4. Create a new map with a penalty
  • 5. Add OX map to FLD file
  • 9. Dock