Tutorials

Redocking

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
[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

Consensus Scoring analysis on two inhibitors docked in Aurora-A protein

Download tests folder here
[PyMOL workspace] - File - Open ... → Open all files in the directory "/tests/consensus_docking/".

OR

[PyMOL workspace] → File → Get PDB → Type "3uo4" and "3uoh"
[PyMOL workspace] → Extract the co-crystallized ligands as objects "obj01" and "obj02"
[PyMOL workspace] → Delete object "3uoh"
[PyMOL workspace] - File - Open
Vina Tab → Receptors Tab → Import from PyMOL → check “3UO4” → Import
Receptors tab → check All → Generate receptor → select “01_3uo4_Vina” → Set
Ligands tab → Import from PyMOL → check All → Import
Ligands tab → check All → Generate Ligand → select “01_obj01_Vina” and “02_obj02_Vina” → Set
Grid settings tab → Import Objects from PyMOL → Selection: “obj01” → X = 4; Y = 4; Z = 4 → Set in Docking Tab
Docking Tab → ALLvsALL → Receptors: “01_3uo4_Vina” → Ligands: “02_obj02_Vina” and “01_obj01_Vina” → Poses: 10 → Run Docking

Smina Tab → Receptors Tab → Import from PyMOL → check “3uo4” → Import
Receptors tab → check All → Generate receptor → select “01_3uo4_Smina” → Set
Ligands tab → Import from PyMOL → check All → 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_3uo4_Vina” → Ligands: “02_obj02_Vina” and “01_obj01_Vina” → Poses: 10 → Run Docking

DATA ANALYSIS → Consensus Scoring → Consensus Score: “Average of Auto-Scaled Scores” → Start
DATA ANALYSIS → Consensus Scoring → check Filter by RMSD
Consensus Matrix Window → change RMSD threshold by moving the slider → Update Consensus Table