mol_model_course_2023

Workshop: Introduction to Docking

Description

• 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

Jupyter notebook

• analyse.ipynb
• docking.ipynb

  Required software and resources

• Access to a Jupyter notebook evironment with Python 3, MDanalysis, nglview and oddt libraries
• Access to Newton cluster with MDanalysis, nglview and oddt installed or install MDanalysis, nglview and oddt at your local workstation. See https://oddt.readthedocs.io/en/latest/rst/oddt.html

Learning resources

• oddt Documentation https://oddt.readthedocs.io/en/latest/rst/oddt.html
• AutoDock Vina Documentation https://oddt.readthedocs.io/en/latest/rst/oddt.docking.html

Assignments

Perform protein-ligand docking.

1. Save protein and ligand PDB structures into different files (if need).
2. Configure docking parameters.
3. Perform protein-ligand docking via AutoDock Vina.
4. Calculate RMSDs for all conformations.
5. Compare results and visualize the best conformation.

Suggested problem sets

Each student should take a unique PDB structure at his/her own discretion.

Troubleshooting

• Consult with the seminar protocol/recording
• Ask questions in Slack