When doing docking using AutoDock Vina, there is one step : "Run Vina". This step is where we can set our "Vina Search Space". We can set the gridbox for docking of ligands
Center: x, y and z
Size: x, y and z.
Question on, we should run the docking based on which option below?
1st Option: run the vina search space by default value
2nd Option: reset the gridbox where we focus on "whole target protein" structure. This step is so that we can see more interaction site between protein and ligand when we focus on whole protein for docking.
3rd Option: reset the gridbox where we only select the active sites (that is predicted through "binding site prediction", for example, using metapocket and other predictor tool). This step meant we only focus on docking that is shown on the selected active sites. But this step, we cannot know more interaction on other site in whole protein.
Which option is better? And please kindly provide the reason.
And, is there any article stating that we should focus on whole protein structure or selected active sites for docking?
Thank you very much :)
I think it depends on the study you are carrying out. If you are testing a new small molecule for its binding properties better go for the active site already reported in the literature, because it would be easier for you to compare how much efficiently your molecule is binding than that of the already reported molecule. If your study is to finding out different sites of a protein molecule that can bind to a given small molecule (which often leads to side effects), better go for 'focus on whole target protein'.