Workshop: Introduction to Docking
- We will outline basic methods of docking with AutoDock Vina using Open Drug Discovery Toolkit.
- Duration: 90 minutes
- Objectives: be able to
- Understand how to configure docking parameters
- Convert pdb files to pdbqt
- Perform docking with AutoDock Vina in Python
- Understand and analyse docking results
Perform protein-ligand docking.
- Save protein and ligand PDB structures into different files (if need).
- Configure docking parameters.
- Perform protein-ligand docking via AutoDock Vina.
- Calculate RMSDs for all conformations.
- Compare results and visualize the best conformation.
Suggested problem sets
Each student should take a unique PDB structure at his/her own discretion.
- Consult with the seminar protocol/recording
- Ask questions in Slack