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Docking

Tutorial: Installing Autodock Vina on Windows

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Autodock vina on windows

We have provided several tutorials on Autodock Vina software [1] including its installation on Ubuntu. This article is a guide to install Autodock Vina on Windows 10.

Before installing Vina, make sure you have enough free space available in a drive where you are going to install.

Downloading MGLTools

You can either download a zip file or an installer of MGLTools. Here, we will install using the Windows installer. Download it from here. It can run on both 32-bit and 64-bit supporting architecture.

Downloading Autodock Vina

Download .msi of Autodock Vina from here.

Installing MGLTools

Double click on the download file. It will ask to accept the agreement followed by the location to install MGLTools. Accept the agreement and select an appropriate drive and folder to install.

Installing Autodock Vina

Double click on the downloaded msi file. Select an appropriate location to install and wait to finish. This will create a new folder named ‘Vina-xxx‘. There you will find vina.exe that will be required at the time of its execution.

Now, you can see shortcuts would have been created on your desktop. Double click Autodock-Tools shortcut to start graphical user interface. There you can prepare your receptor and ligands for docking. For this, you can refer to blind docking and site-specific docking articles.

Running Autodock Vina

After you prepare all files, keep them in a same folder. I would suggest you to run keep them anywhere other than C:\ drive. Open a command prompt, provide the full path to vina executable (vina.exe), and run the command. The procedure and command to run Vina on Windows are explained in this article.


Reference

  1. 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.

Tariq is founder of Bioinformatics Review and CEO at IQL Technologies. His areas of expertise include algorithm design, phylogenetics, MicroArray, Plant Systematics, and genome data analysis. If you have questions, reach out to him via his homepage.

Bioinformatics Programming

How to sort binding affinities based on a cutoff using vs_analysis.py script?

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How to sort binding affinities based on a cutoff using vs_analysis.py script?

Previously, we have provided a Python script (vs_analysis.py) to analyze the virtual screening (VS) results of Autodock Vina. Now, we have updated this script to sort binding affinities based on user inputted cutoff value. (more…)

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Docking

Virtual Screening using Autodock Vina: Frequently Asked Questions & Answers for Starters

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Virtual Screening using Autodock Vina: Virtual Screening: Frequently Asked Questions & Answers for Starters

Virtual Screening (VS) is one of the important techniques in bioinformatics. It can be easily performed using Autodock Vina. We have provided detailed articles on this topic. In this article, we are trying to answer some FAQs for beginners. (more…)

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Docking

[Tutorial] How to perform docking of zinc metalloproteins using Autodock Vina?

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[Tutorial] How to perform docking of zinc metalloproteins using Autodock Vina?

Proteins containing zinc atoms are docked in a different way than that of the normal simple proteins. Zinc atoms must be considered by a force field during the docking process. In this article, we are going to dock zinc metalloprotein with a ligand using Autodock Vina [1]. (more…)

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