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.
At first, a few of the basic questions regarding VS are explained below followed by the FAQs regarding VS in Autodock Vina.
Question: What is VS in bioinformatics?
Question: What is the basic methodology involved in VS in bioinformatics?
Question: Is VS using Autodock Vina possible? If yes, then how?
Answer: Yes, VS using Autodock Vina is possible. It can be done two ways, either by installing Raccoon plugin or by using a Perl script. The plugin will run on a server.
Question: How can I perform docking without the Raccoon plugin?
Answer: If you don’t have any cluster computer, then you can easily use Perl script. Since you will have to prepare multiple ligands/proteins or maybe a complete database, therefore, you can use Python scripts for that. Now, the result log files will be huge in numbers. For this purpose, there is another Python script. Here are links to some of the articles that will guide you.
Question: How to download compounds for VS?
Question: How to install the Raccoon2 plugin for VS?
Question: How do I define ligand names for virtual screening?
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…)
[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 . (more…)