Docking of spike protein of bat coronavirus with ligand 1

ASSIGNMENT NO 03

Principles of biochemical engineering

Docking

Naeema khanum

International Islamic university,

Islamabad.
Docking of spike protein of bat coronavirus with ligand 2

Steps of docking:
 Select a target protein and ligand.

 Carry out preparation of protein and ligand.

 Select the docking site in the protein.

 Carry out protein-ligand docking using docking tool.

 Different ligand poses are generated.

STEP 1: SELECTION OF PROTEIN AND LIGAND:

PROTEIN SELECTED:Spike Protein of RaTG13 Bat Coronavirus

LIGAND: remdesivir

The protein cen be selected from any of the protein database like RCSB PDB and

then can be downloaded in pdb format like shown below:

Docking of spike protein of bat coronavirus with ligand 3

The ligand can also be selected and dowloaded from any database like pubchem or

chem spider ,3D view but in sdf format it would be dowloaded but would be

converted to pdb using PYMOL.

Docking of spike protein of bat coronavirus with ligand 4

STEP:2 PREPARATION OF PROTEIN AND LIGAND:

The protein and ligand would be prepared by editing in the autodock vina tool as shown
below:
Docking of spike protein of bat coronavirus with ligand 5

Protein preparation involve removing water,adding koulman cahrges,adding non polar

hydrogens.

Ligand is simply dragged and dropped.

Docking of spike protein of bat coronavirus with ligand 6

Now protein is also dragged and dropped with it ,then the view of before docking will appear

And it would be like :

Docking of spike protein of bat coronavirus with ligand 7

STEP 3 SELECTION OF DOCKING SITE IN PROTEIN:

In order to find docking site on protein you need to form grid file .from the grid file

configuration file is also formed and then commands are given to command prompt as

autodock vina have not any software yet built to measure docking site.
Docking of spike protein of bat coronavirus with ligand 8

Now commands will be given to command prompt and it will compute poses ,afinity etc for
docking.
Docking of spike protein of bat coronavirus with ligand 9

STEP 4 PROTEIN LIGAND DOCKING USING DOCKING TOOL:

Log file ,output pdbqt file will appear in your specified folder and when you drag the output

file aling with protein you will be able to view the following interaction:
Docking of spike protein of bat coronavirus with ligand 10

STEP 5 VIEW DOCKING:

Nine different poses of ligand can be seen just be presseing right and left arrows on the

keyboard.

Different format view like surface cartoon and ring structure can also be viewed using pymol

In above figure surface view is shown.