Tutorials
How to redock ADP in Aurora-A with RxDock.
- Open PyMOL
- [PyMOL workspace] - File → Get PDB → Type “1OL5” → Download
- [PyMOL workspace] - Select ADP → Action (A) → extract object
- [PyMOL workspace] - Plugin → DockingPie 1.0
- RxDock Tab → Receptors Tab → Import from PyMOL → check “1OL5” → Import
- check “1OL5 (1) PROTEIN” → Generate receptor
- select “01_1ol5_RxDock” → Set
- Ligands Tab → Import from PyMOL → check “obj01” → Import
- check “obj01 (1)” → Generate Ligand
- select “01_obj01_RxDock” → Set
- Grid settings Tab → check ‘Reference ligand method’ → Receptor: “01_1ol5_RxDock” → Reference Ligand: “01_obj01_RxDock” → Generate Cavity
- visualize “prm_file0_cav1” → Set
- Docking Tab → Available cavities: “prm_file0_cav1” → Receptors: “01_1ol5_RxDock” → Ligands → “01_obj01_RxDock” → Run Docking
- Results Tab → double-click on the table to visualize the docked pose in PyMOL
- Calculate RMSD → Import from PyMOL → select “obj01” → Calculate RMSD
Docking of two inhibitors in two different crystal structures of HIV-1 protease ("1BDR" and "1BDQ").
- Download tests folder [here](link to tests folder)
- [PyMOL workspace] - File - Open ... → Open all files in the directory "/tests/cross-docking_HIV/".
OR
- [PyMOL workspace] → File → Get PDB → Type "1hvr" and "1bdq"
- [PyMOL workspace] → Extract the co-crystallized ligands as objects "obj01" and "obj01"
- Smina Tab
- Receptors tab → Import from PyMOL → check All → Import
- Receptors tab → check All → Generate receptor → select “01_1bdq_Smina” and “02_1hvr_Smina” → Set
- Ligands tab → Import from PyMOL → check All V Import
- Ligands tab → check All → Generate Ligand → select “01_obj01_Smina” and “02_obj02_Smina” → Set
- Grid settings tab → Import Objects from PyMOL → Selection: “obj01” → Use as a Reference → Set in Docking Tab
- Docking Tab → ALLvsALL → Receptors: “01_1bdq_Smina” and “02_1hvr_Smina” → Ligands: “02_obj02_Smina” and “01_obj01_Smina” → Poses: 10 → Run Docking