Docking
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 most primary use of Autodock Vina is for different types of docking including site-specific, blind docking, protein-ligand, and so on.
- Besides docking, Autodock Vina (Autodock Tools) helps in editing protein and ligands including their structure modifications.
- It is also used for the virtual screening of 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 basic uses of Autodock Vina.
References
- 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 chemistry, 31(2), 455-461.
Further Reading
How to perform docking in a specific binding site using AutoDock Vina?
A configuration file is one of the required files for docking using Autodock Vina. In this article, we are going to generate a config file using Autodock Tools GUI [1]. (more…)
Autodock [1] is most widely used for docking. To accelerate the docking process, especially, during virtual screening, Autodock-GPU [2] provides great help. In this article, we are going to install Autodock-GPU on Ubuntu. (more…)
Pyrx is a bioinformatics tool to perform virtual screening [1]. We previously provided an article on performing simple protein-ligand site-specific docking using Pyrx. In this article, we are going to perform virtual screening using Pyrx. (more…)
You must be logged in to post a comment Login