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

in Tips & Tricks by

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 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]
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Muniba is a Bioinformatician based in the South China University of Technology. 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

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