.Molecular Docking to study Protein- Ligand interaction.

Step I - Preparing target protein

AutoDock expects that the input protein has polar hydrogens and that all the water
molecules have been removed. We will get errors if this is not the case.

Protein.pdb file is opened in ADT

File->Read Molecule

We can rotate the structure with the middle mouse button. Zoom with the middle mouse
button while holding down the shift key.

Polar hydrogens are added to the target structure

Edit->Hydrogens->Add->Polar only->Ok
Kollman charges are added to the peptide
Edit->Charges->Add Kollman Charges
The structure is saved
File->Save->Write PDB

Figure 3.5: HSG protein loaded in ADT.

Step II - Initializing ligand for docking

The Protein is hidden from the view

Display->Show/Hide Molecule
Uncheck the protein name from the dialog box.
 The ligand file is loaded.
Ligand->Input->Open...
Change the file type to .pdb, choose the ligand file saved in .pdb format->
Open

ADT initializes the ligand file and adds gasteiger charges to the ligand structure. If the
ligand was a peptide it would have added Kollman charges.

Figure 3.6: Ligand file is initialized and summary of actions for the ligand is displayed.

Detecting the root of the ligand.

Ligand->Torsion Tree->Detect Root...
View rotatable bond
Ligand->Torsion Tree->Choose Torsions...
Set rotatable bond (Active torsions) to 6 while allowing the fewest atoms to
move. Ligand->Torsion Tree->Set Number of Torsions
The Ligand is saved in PDBQT file format as Ligand.pdbqt.
Ligand->Output->Save as PDBQT

Step III - Preparing Grid map

Grid is placed on the target active site and should contain all atoms that could possibly
interact with the ligand. It should be large enough to allow the ligand to fully rotate.
 Target protein is chosen in which the ligand will dock.
Grid->Macromolecule->Choose..(protein)

Select the protein target prepared in step 1. Immediately after the file opens ADT opens
the file save dialog to save the initialized target protein in .pdbqt format. This structure
is saved in the directory in which we will run AutoDock.

Setting the Map types that will be used for the grid.
Grid->Set Map Types->Choose Ligand.(Ligand)
Setting the Grid Box position and size.

Grid Box...

(Dimension: 60X60X60; Spacing 0.408; X centre: 15.438,Y centre : 23.703, Z centre :

4.245)

Figure 3.7: Grid options widget

Saving the current grid positioning

File->Close Saving Current

Saving Grid file

 Grid->Output->Save GPF.

In the file save dialog explicitly type Grid.gpf to save the grid parameter file.

Running AutoGrid
Run->Run AutoGrid..

Step IV- Setup docking parameter file

Setting the protein target to be docked

Docking->Macromolecule->Set filename->protein.pdbqt
Ligand is selected which is to be docked
Docking->Ligand->Choose (Ligand)

A ligand parameters window opens and all parameters at the default values are selected.

Setting search parameters

Docking->Search Parameters->Genetic Algorithm...

Following changes are made to the parameters:

Number of runs -> 10

Population size -> 150

Rest of the parameters left at the default values

Docking parameters are set to default

Setting the Docking output parameter file
Docking->Output->Lamarckian GA.

Docking Parameter file is explicitly saved as Dock.dpf.

Running AutoDock
Run->Run AutoDock.

NOTE: AutoDock and AutoGrid have to be run in the same directory as Ligand.pdbqt,
HBx.pdbqt, Grid.gpf and Dock.dpf.

Step V - View Docked conformation energies

 After the AutoDock completed its run, the result is viewed in ADT.
Analyze ->Dockings->Open->Dock.dlg
Macromolecule is loaded into view
Analyze->Macromolecule->Choose..(protein)
Viewing the conformations
Analyze->Conformations->Play, ranked by energy
Choose best conformation
Set Play Option->Build Current
Save best conformation file in .pdb format
Analyze- show interaction