Defining binding site Now we will define the binding site in the protein. Look at the panel in the left corner of Vina window. You will see the name of the protein written there. Click on it once, then it will show you the chains present in the structure, but since we have deleted all the chains except the chain A, so there is only one chain, i.e., chain A. Click on it, then it will display all the residues present in the chain. Now scroll down and look for your desired residues. For example, in this protein, we will look for Tyr150, Lys199, Arg222, Arg257, and His242 because this is the binding site of CMPF in human serum albumin and we want to bind another ligand in the same position. On the right side of dropdown of all residues, we can see some squares and oval shaped images. By clicking these, we can see the selected residues in different types, such as on clicking “R”, the residue will be displayed in ribbon-shaped, but we will only select all the residues by clicking “S”. Now the selected residues will appear differently such as yellow in color. Now we have selected all the residues and we will define the grid box which can enclose all these residues inside itself. Defining Grid Box for docking
Now we will define the specific site for binding of a ligand in the protein. In blind docking, we do not need to define a specific site in the protein for the ligand to bind, because we do not know the binding site, so we enclose the whole protein into the grid box. But here we already know the binding site in this protein, therefore, we will define binding site for the ligand in the grid box. 1. Click “Grid” --> click “Grid Box”. You will see a small window in which you can see x, y, and z coordinates. 2. Now try to adjust the grid box by scrolling the three coordinates, such that it covers all the selected residues. 3. After adjusting the grid box, click “File” --> click “Output Grid Dimension File” --> save this file as grid.txt in the same folder. 4. Click “File” --> Click “Close saving current”. 5. Now close the Autodock Vina. You will get the grid file as follows:
Preparation of Configuration file AutoDock Vina requires an input configuration file which contains all the information of the parameters used in configuring the docking including the name of the protein and the ligand. The configuration is as follows: receptor= protein.pdbqt ligand= SO.pdbqt
center_x= 4.402 center_y= -8.060 center_z= 8.874
size_x= 66 size_y= 56 size_z= 54
out= vina_outSO.pdbqt log= logSO.txt
grid.txt exhaustiveness= 8
Protein spacing 0.375 npts center
66 56 54 4.402 -8.060 8.874
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