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What is involved in the discovery of a ligand "inside" a protein?
Title
Question
When we add a ligand, it appears "inside" the protein. Why is this the case? 
Is it possible to somehow adjust the field so that there is a space between the ligand and the protein? 

AutoDock4 Running-AutoGrid 03-04 min 10-20 sec 09-08-24, 3:53 p.m. Ivajull

Answers:

 We have used the known receptor-ligand system, downloaded from PDB database for demonstration, hence you will see the binding of ligand with the receptor.
09-08-24, 4:03 p.m. snehalathak

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