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Virtual Screening: Frequently Asked Questions & Answers for Starters

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Virtual screening: FAQs for starters

Virtual screening can be difficult for beginners. Here are some FAQs for starters that can help you overcome small issues.

In this article, I have collected some of the most Frequently Asked Questions while performing virtual screening. You have to consider a lot of factors before performing an actual docking on a protein with multiple ligands.

Question: How to download compounds for virtual screening? 

Question: How to know which database to download for virtual screening?

Question: How to prepare multiple ligands for virtual screening?

Question: How to know the binding pocket of a predicted structure of a protein for VS?

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

Question: Error: Could not open file ligands.txt

Question: Error: Could not open file “protein.pdbqt” for reading

These are a few FAQs for beginners in bioinformatics. If you have any other query then feel free to post a question in our community.

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?

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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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