Connect with us

Docking

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

Published

on

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.

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?

Answer: 

What is Virtual Screening in Bioinformatics?

Question: What is the basic methodology involved in VS in bioinformatics?

Answer: 

Virtual Screening Methodology for Structure-based Drug Designing

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.

How to perform virtual screening using Autodock Vina?

Prepare receptor and ligand files for docking using Python scripts

vs_Analysis.py: A Python Script to Analyze Virtual Screening Results of Autodock Vina

Question: How to download compounds for VS?

Answer: 

How to download small molecules from ZINC database for virtual screening?

Question: How to install the Raccoon2 plugin for VS?

Answer: 

Raccoon2: A GUI facilitating virtual screenings with Autodock and Autodock Vina

Question: How do I define ligand names for virtual screening?

Answer:

How do I define ligand names for virtual screening?

Dr. Muniba is a Bioinformatician based in New Delhi, India. She has completed her PhD in Bioinformatics from South China University of Technology, Guangzhou, China. 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

Bioinformatics Programming

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

Published

on

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…)

Continue Reading

Docking

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

Published

on

[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…)

Continue Reading

Docking

How to generate config file for docking using Autodock Tools?

Published

on

How to generate config file for docking using Autodock Tools?

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…)

Continue Reading

LATEST ISSUE

ADVERT