Hello,
I am using autodock4 for blind docking of ligand-protein.the size of protein is very large, its contain 5 domains. now i want to make large grid box that cover the whole macro-molecule but according to the protein X, Y and Z coordinates, its cover approx half of the protein structure. i have select 1A spacing with maximum number of points in all dimensions (I.e. 126).
Please guide me is there any way to cover my complete protein structure with the grid box. i have attached my protein structure.
Hi
I suggest you to look for binding site (http://ftsite.bu.edu/) first then make grid on that site to dock.
If you wanna do blind docking, go for random sampling.
Dear Sidra
There are two approaches to solve this problem.
First, Increasing grid point distances (the default is 0.375A).This effects on accuracy of your results directly(not suggested).
Second, Performing Two or more different docking process. For each docking , the grid box covers a part of macro molecule.Eventually, you can easily find the binding site by comparing the results.
Best
Dear Hamed and Navneet,
thank you so much for your guidance.
Hamed: In second option you are talking about "the grid box covers a part of macro molecule." it's not very clear to me
please explain it.
One can generate several overlapping boxes and perform docking calculation for each of them.
You can get rid of that problem using our Blind Docking server:
http://bio-hpc.ucam.edu/aquiles/
you can do a blind docking in Arguslab software but if you patient auto dock is good
Its better for you firstly done a blind docking or defined the overlap grid boxes with less size in different area of protein.its decrease your customize time and involve your computer memory
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