Docking - Page 11

Docking is a mechanism to analyze the interaction of two or more molecular structures (i.e., receptor and ligand).

Site-specific docking: Frequently Asked Questions & answers for starters


I have been getting several E-mails from researchers and students alike regarding in-silico docking. Most questions are similar in nature, so I thought of answering them once and for all. In this article, I have collected some frequently asked questions and provided the link to their answers present in our question-answer section of Bioinformatics Review.

It is good to have questions in mind and they can be solved in a way as quoted by Sir Einstein:

“We cannot solve our problems with the same thinking we used when we created them.”

In this article, I have collected some of the most Frequently Asked Questions while performing site-specific and/ or blind docking. You have to consider a lot of factors before performing an actual docking on a protein with a specific ligand.

Question: How do you predict protein’s binding sites? 

Question:  What is the difference between the blind docking and binding site based docking?

Second thing, if I have to find the distance between a ligand and any residue in the receptor molecule. Do I have to take the central atom distances or minimum distance between any two atoms of the ligand and receptor molecule can be considered ?? 
If these are not the questions you are looking for, then feel free to ask in our ‘Bioinformatics Discussion‘ section or write to [email protected]

How to perform docking in a specific binding site using AutoDock Vina?


AutoDock Vina is a bioinformatics tool which is used to perform in- silico docking of proteins with a ligand. It provides many options depending on the needs of a user. This tool offers blind docking and binding in a specific pocket as well, which is sometimes more demanding when the binding site is already known. This article will guide you to dock a protein with a ligand in a specific binding site/ pocket. Keep Reading

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