Connect with us

Docking

Blind Docking vs Site-specific Docking

Tariq Abdullah

Published

on

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.

Docking

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

Dr. Muniba Faiza

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?

Dr. Muniba Faiza

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

Docking

How to install Autodock on Ubuntu (Linux) with CUDA GPU support?

Dr. Muniba Faiza

Published

on

How to install Autodock on Ubuntu (Linux) with CUDA GPU support?

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…)

Continue Reading

LATEST ISSUE

ADVERT