I want to screen a protein having a manganese atom in its active site. I would like to know which Autodock tool will give better results?
I previously used Autodock Vina but was not satisfied with some of the know poses for some of my ligands especially there was a hydroxymate group of the ligand which was not chelating the metal atom.
In the paper Article AutoDock4(Zn): An Improved Auto Dock Force Field for Small-M...
: talking the Autodock force field it is said:“is accurate enough for magnesium ion interactions, it is not sufficient to properly describe zinc coordination preferences.”
In the periodic table, in terms of atomic number, manganese falls between Mg and Zn but closer to Zn.
For my case (protein contain Mg) I've used vina and it gave me better result.
Hi Bakary,
I previously docked tridentate ligands to Manganese protein by use of AutoDock 4, which gave satisfactory results.
Article Binding mode prediction and inhibitor design of anti-influen...
Or you can try idock, which is inspired by Vina and can treat Mn ion.
https://github.com/HongjianLi/idock
https://github.com/HongjianLi/idock/archive/v2.2.2.zip
It is non-standard, which means you have to standardize it. If you have a control ligand, you may vary the partial charge on Mn and check if it is reproducing the correct coordination distances. Generally, for a divalent cation, a partial charge in the range of +0.6 to +0.8 should work.
Thank you for you replies.
@Uttam
According to Vina manual (http://vina.scripps.edu/manual.html):
"AutoDock Vina ignores the user-supplied partial charges. It has its own way of dealing with the electrostatic interactions through the hydrophobic and the hydrogen bonding terms. "
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