Hi Bioinformatics review, I am an undergraduate chemistry student from Malaysia. I’m very new to bioinformatics as I need to do research using molecular docking studies, therefore I’m very lacking in regards to ADT software.
I want to ask if the grid box that is automatically generated by ADT is actually the active site of the protein, or it is randomly generated? Can I use the grid box generated without editing any of the values generated (as shown in tutorial here: How to perform docking in a specific binding site using AutoDock Vina? – Bioinformatics Review)
No, the default grid box is not the active site of the protein. You have to read about the protein of interest to find out the actual active site of that protein. Read the following article: