5.1 Change Box specifications on AMDock PyMol plugin - Valdes-Tresanco-MS/AMDock-win GitHub Wiki

Although several methods to determine the optimal search space have been implemented in AMDock, sometimes the user might want to modify the box specifications. To do so, a PyMOL plugin called “AMDock Box Builder” can be used. Once the user modifies one of the box specifications, AMDock will automatically activate the “user-defined box” method and the user will control the whole process.

It’s recommended to be cautious when modifying the box specifications from the “Automatic” method since AMDock will activate automatically the “user-defined box” method and no longer perform a docking run for every predicted binding site.

Receptor (4uwh.pdb) and ligand (ligand.pdb) files are available in Installation_path/Doc/Tutorial/IV_AMDock_Box_Builder folder.

  1. Open AMDock program
  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/IV_AMDock_Box_Builder/4uwh.pdb)
  7. Choose the ligand file (Installation_path/Doc/Tutorials/IV_AMDock_Box_Builder/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, pick “Center on Residue(s)”. A text box will appear where residues should be specified by following this notation:

CHAIN:RESIDUE1:NUMBER; CHAIN:RESIDUE2:NUMBER…

AMDock checks automatically if those residues exist in the receptor.

In this tutorial, the following residues were chosen:

A:ILE:634; A:TYR:670; A:PHE:684; A:PHE:758; A:ILE:760

  1. Press “Define Search Space” button

Once the search space is defined, you can see the box by pressing the button “Show in PyMOL”. In this case, the receptor is represented as cartoon, binding site residues in sticks and the object generated in AutoLigand as mesh representation.

  1. Find AMDock in the PyMOL menu bar and click “AMDock Box Builder”
  2. In the “AMDock Box Builder” window, observe the initial coordinates of the box (20.1833; -13.8611; -23.2944) as well as the dimensions (19; 19; 19Å). Then, increase the size (23; 23; 23Å) and move it in the x-direction (21.6000; -13.8611; -23.2944) and you will see a new box (Target_box; white) along with the reference box (in magenta).

  1. Click “Save Box Info” and check in the PyMOL command input area that the new specifications have been introduced successfully. Close PyMOL after that and check that the new specifications are written in the Search Space.

A similar procedure can be applied to modify the two search spaces when performing “off-target” docking.

  1. Press “Define Search Space” button and now proceed with the docking run