4.2.4 Automatic mode using AutoDock Vina - Valdes-Tresanco-MS/AMDock-win GitHub Wiki

This option (also known as “blind docking”) is recommendable only when you have no idea where the binding site is.

Receptor (4uwh.pdb) and ligand (ligand.pdb) files are available at Installation_path/Doc/Tutorials/I_Simple_Docking/4.Box_Auto folder. The crystal structure of the complex (complex.pdb) is available as well for comparison purposes.

  1. Open AMDock program or Create a new project in “Results Analysis”
  2. Select Autodock Vina
  3. Set the Project Name (default Docking_Project)
  4. Set the Location for Project and push the button "Create Project"
  5. Check that “Simple Docking” checkbox is selected (It is checked by default)
  6. Choose the receptor file (Installation_path/Doc/Tutorials/ I_Simple_Docking/4.Box_Auto/4uwh.pdb)
  7. Choose the ligand file (Installation_path/Doc/Tutorials/ I_Simple_Docking/4.Box_Auto/ligand.pdb)

Before going to the next step, go to the configuration tab and check “Ligand Protonation” with OpenBabel.

  1. Press “Prepare Input” button
  2. Then, for defining a search space, choose “Automatic”.
  3. Press “Define Search Space” button (and go for a coffee)
  4. Once AutoLigand is done, a table showing both the volume and the EPV (Energy per Volume) for every predicted binding site will appear.

You can see the box by pressing the button “Show in PyMOL”. In this case, the receptor is represented as cartoon, binding site in transparent surface and the objects generated in AutoLigand as sticks. Only one box is showed for better clarity.

Note: If you want to modify the box, you can use the AMDdock plugin in PyMOL. More details about this procedure here.

  1. Press “Run” button (and go for a coffee again)

An independent docking run will be performed in every site predicted by AutoLigand.

  1. When docking run ends, “Results Analysis” tab will appear automatically. There, you will observe a summarizing table with Binding Energies, Estimated Ki values, and Ligand Efficiencies.

Each of the rows in the final table corresponds to the better pose predicted for that binding site.

  1. In the results table, just the first pose is selected. Press the button “Show in PyMOL” in the bottom left corner to visualize the complex. _ If you want to see all the predicted poses, just select all the poses in the result table and press “Show in PyMOL”._

  2. The crystal structure can be superposed on the predicted structure. Press “Open” in the upper left corner in PyMOL and find the X-ray structure (Installation_path/Doc/Tutorials/I_Simple_Docking/4.Box_Auto/complex.pdb)

  3. A detailed report of the entire process can be seen on the right side of the screen, which allows for tracking all the results from different programs and algorithms. This log file can be saved in case an error occurred and sent to the developers.