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Autodock Vina: Uses & Applications

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Autodock Vina: Uses & Applications

Autodock Vina [1] is one of the most widely used bioinformatics software for computational docking. For beginners and those who are new to the field of bioinformatics, such software may appear confusing without having an initial idea of what this software actually used for. In this article, we have discussed some of the primary uses and applications of Autodock Vina software.

Some of the primary uses of Autodock Vina are as follows:

  • The primary use of Autodock Vina is for different types of docking including site-specific, blind docking, protein-ligand, etc.
  • Besides docking, Autodock Vina (Autodock Tools) helps in editing protein and ligands including their structure modifications.
  • It is also used to screen large or small libraries of molecules.
  • It is easily accessible on Linux as well as on Windows.
  • The GUI of Autodock Tools helps can be used to visualize interactions between the receptor and the ligand.
  • It can be used to analyze the docking results.
  • Easy conversion of PDB to PDBQT format.
  • It is used to perform rigid as well as flexible docking.
  • Easy analysis of virtual screening results.

These are some of the primary uses of Autodock Vina.


References

  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.

Further Reading

How to perform virtual screening using Autodock Vina?

Video tutorial: How to install Autodock Vina on Ubuntu?

Tutorial: Vina Output Analysis Using PyMol

How to perform docking in a specific binding site using AutoDock Vina?

 

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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