Bioinformatics Tools Training Program

AutoDock is an automated procedure for predicting the interaction of ligands with
biomacromolecular targets. The motivation for this work arises from problems in the design of
bioactive compounds, and in particular the field of computer-aided drug design. Progress in
biomolecular x-ray crystallography continues to provide important protein and nucleic acid
structures. These structures could be targets for bioactive agents in the control of animal and plant
diseases, or simply key to the understanding of fundamental aspects of biology. The precise
interaction of such agents or candidate molecules with their targets is important in the development
process.

AutoDock has applications in:
• X-ray crystallography;
• structure-based drug design;
• lead optimization;
• virtual screening (HTS);
• combinatorial library design;
• protein-protein docking;
• chemical mechanism studies.

AutoDock 4.0 can be compiled to take advantiage of new search methods from the optimization
library, ACRO, developed by William E. Hart at Sandia National Labs. We have also added some
new features to our existing evolutionary methods. We still provide the Monte Carlo simulated
annealing (SA) method of 2.4 and earlier.

Why Use AutoDock?
AutoDock has been widely-used and there are many examples of its successful application in the
literature. It is very fast, provides high quality predictions of ligand conformations, and good
correlations between predicted inhibition constants and experimental ones. AutoDock has also been
shown to be useful in blind docking where the location of the binding site is not known.

Procedure
1. Open the Autodock software by clicking on Autodock icon from your desktop.
2.Read the downloaded PDB molecule 1E7U in the work space panel by clicking on the tab
“File“ and then select “Read molecules”
3.PDB files can have errors such as missing atoms, chain breaks, water molecules etc. which is
needed to be corrected. Select all water molecules which obstruct the accuracy of docking
procedure.
4.Click on the “Edit” tab and select “Delete Water” to delete the water molecules from the receptor
molecule
5. For adding Hydrogens to satisfy valency, Click on the “Edit” tab and select “Hydrogen” and then
select “Add” option
6. Now select “Polar Only” -> “noBondOrder”->”Yes” respectively and then click on the “Ok”
option
7. Click on the “Grid” option and select “Macromolecules” and select Choose option for selecting
the molecule
8. By clicking on the respective molecule will display the details of non bonded atoms, non polar
hydrogen atoms and non integral charge on the molecule. After that save the molecule in PDBQT
format.
9. To set grid parameters, go to “Grid” . A “Grid Option” message appears which helps the user to
change the grid point per map in all positions. It sets the 3D space for better binding conformation.
The maximum value that can be given by the Autogrid is 126.
10. Next step is to prepare the ligand molecule for docking. Open the ligand miolecule by clicking
on the “Ligand” option and select “Input” and click on “Open”. Select the downloaded molecule
and open it in the work space panel
11.The receptor molecule and ligand molecule can be viewed separately by clicking on dashboard
which is displayed on the left side of the work space panel. By selecting the required molecule will
display it in work space panel. The other options will enable us to view in other formats too
12.To choose Torsions, click on the “ligand “ -> “Torsion Tree” ->”Choose Torsions” which will
display the number of rotatable bonds. The rotatable bonds is displayed in green color, non-rotatable bonds in magenta color and unrotatable bonds in red color. To make a non – rotatable bond to
rotatable, click on the bond itself
13.The output can be saved inPDBQT format. For that click on the “Ligand” -> “Output” ->”Save
as PDBQT” , so that it can be saved along with the receptor molecule in the same folder itself
14.For running the Vina program, command prompt is used, “vina help” prints the different options
necessary for running the program. It includes commands for receptor, ligand and so on.The
configuration file is wriiten in a text document with the following format
15. For running Autodock Vina, vina.exe –config conf.txt –log log.txt can be used as the script as
shown in figure 14, which will create an outout file of the ligand and a log file along with other
files.