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Docking

Blind Docking vs Site-specific Docking

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Blind docking vs site-specific docking

We have provided several tutorials on docking including both types: blind docking & site-specific docking using Autodock Vina. In this article, we are going to compare both methods of docking.

Both types of docking have their own merits and demerits. It completely depends upon your study which type of docking you select.

Basic Comparison

Parameters Blind Docking Site-specific Docking
Binding pocket Helps to find out Known or predicted
Structural details Unknown Known or Predicted
Catalytic/ Binding residues Unknown Known or predicted
Ligand Docked with whole protein Docked in the binding pocket
Best conformation Software algorithm finds the best conformation of ligand everywhere in the protein. Software algorithm finds the best conformation of a ligand inside the binding pocket.
Grid box The whole protein is enclosed inside the grid box. The binding pocket is enclosed inside the grid box.
Computation time Slow Fast
Advantage Identification of binding sites Precise
Disadvantage Not precise; may show interactions in various sites. Might not be accurate.

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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