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: I have to find the 4 Armstrong neighborhood of a ligand. When I take the receptor molecule without adding hydrogen bonds and find 4A nbd of ligand, it gives one result. But when I first add hydrogens to the receptor molecule and then after finding the 4A nbd of ligand, it obviously gives different results. I want to know which one is better ??