Docking
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. |
After performing computational docking, a question that comes to mind most is “what docking score is considered good or bad”. In this article, we will discuss this in detail. (more…)
Bioinformatics Programming
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…)
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…)
You must be logged in to post a comment Login