Update index.md

workshops/Docking/index.md

@@ -7,34 +7,25 @@
     - Understand how to configure docking parameters
     - Convert pdb files to pdbqt
     - Perform docking with AutoDock Vina in Python
+    - Perform docking with SwissDock
     - Understand and analyse docking results
 
 ## Jupyter notebook
 - [analyse.ipynb](analysis.ipynb)
 - [docking.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](https://oddt.readthedocs.io/en/latest/rst/oddt.html)
+- Access to a Jupyter notebook environment with Python 3, MDAnalysis, nglview, oddt, OpenBabel and Autodock Vina libraries
 
 ## Learning resources
 - oddt Documentation [https://oddt.readthedocs.io/en/latest/rst/oddt.html](https://oddt.readthedocs.io/en/latest/rst/oddt.html)
 - AutoDock Vina Documentation [https://oddt.readthedocs.io/en/latest/rst/oddt.docking.html](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
+- Ask questions in Telegram