How to perform virtual screening using Autodock Vina?

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Virtual screening is used to identify small molecules that are most likely to bind to a target protein. There is various software available for virtual screening including GOLD [1] and GLIDE [2]. Autodock Vina [3] which is a freely accessible software and provides good results can also be used for screening various ligands. Recently, Autodock Vina has provided plugins [4] to facilitate virtual screening. In previous articles, we have provided tutorials for the installation of Raccoon and Raccoon2 plugins on Ubuntu.

These plugins provide a graphical user interface and there is no need to prepare pdbqt files of protein and ligands. You can simply load your target protein and ligand pdb files. In this article, we will use a Perl script or a bash script to screen several ligands for a target protein.

Preparing input files

The docking procedure will be the same as mentioned in previous articles of site-specific docking and blind docking. (Video tutorials: site-specific docking and blind docking).

Prepare pdbqt files of the target protein and all ligands. Save them into the same directory.

Downloading scripts

For Ubuntu/Linux, download these files:

Perl script and bash script.

If you are using Perl script, then list the names of prepared pdbqt files of ligands in a text file.

If you are using the bash script, save the ligands pdbqt files as “ligand_name.pdbqt”, where the name could be any letter. For example, “ligand_3.pdbqt” or “ligand_hydrocl.pdbqt”, and so on.

Further, the configuration file will remain the same as mentioned in previous articles except for the second line, i.e., “Ligand = ligand.pdbqt”.  You can download the configuration file from here (change the coordinates as per your grid dimensions).

For Windows, download this file:

Perl script.

Running Vina for virtual screening

On Ubuntu:

Open the terminal (Ctrl+Alt+T) and type the following command:

$ perl vina_vs_linux.pl

It will prompt for the name of file containing all the names of ligands. Enter the name of the file and continue.

or

$ ./vina_vs.sh

On Windows:

Open command prompt (type cmd in the search tab) and navigate to the folder where you have kept all files including vina.exe. Type the following command:

>perl vina_vs_win.pl

It will also prompt for the name of file containing all the names of ligands. Enter the name of the file and continue.

or

> bash vina_vs.sh

Make sure you have already installed and added Vina in your path on Ubuntu. If not, then follow this tutorial.

References

  1. Jones, G., Willett, P., Glen, R. C., Leach, A. R., & Taylor, R. (1997). Development and validation of a genetic algorithm for flexible docking. Journal of molecular biology267(3), 727-748.
  2. Friesner, R. A., Banks, J. L., Murphy, R. B., Halgren, T. A., Klicic, J. J., Mainz, D. T., … & Shaw, D. E. (2004). Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. Journal of medicinal chemistry47(7), 1739-1749.
  3. Trott, O., & Olson, A. J. (2010). AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of computational chemistry31(2), 455-461.
  4. Forli, S., Huey, R., Pique, M. E., Sanner, M. F., Goodsell, D. S., & Olson, A. J. (2016). Computational protein-ligand docking and virtual drug screening with the AutoDock suite. Nature Protocols, 11(5), 905-919.
Muniba is a Bioinformatician based in the South China University of Technology. She has cutting edge knowledge of bioinformatics tools, algorithms, and drug designing. When she is not reading she is found enjoying with the family. Know more about Muniba

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HOW TO CITE THIS ARTICLE Muniba Faiza (2020). How to perform virtual screening using Autodock Vina?. Bioinformatics Review, 6 (04)
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