We are doing a virtual screening (against 11.000 compounds) using Autodock vina, and one colleague suggested us that we should consider the size of the grid in the docking. Any suggestion (paper) of how to properly stablish the size of the grid in AutoDock Vina?
I would suggest you to use Achilles Blind Docking server (https://bio-hpc.ucam.edu/achilles/), where you do not need to specify neither grid size nor specific residues since it will scan the whole protein surface in order to detect the most probable interaction spots. The user interface is really straightforward and here one of our last application examples in Nat Chem Biol:
https://www.nature.com/articles/s41589-019-0278-6
Hi Carlos javier,
To consider the size of the grid, you should take into account the size of the active site and it would be better if your protein had a ligand in that active site. Usually the size can be 25X25X25, everything depends on your active site.
Calculating an optimal box size for ligand docking and virtual screening against experimental and predicted binding pockets.
Article Calculating an optimal box size for ligand docking and virtu...
Generally box size should be 60x60x60 and the position of the box can be based on the existing ligand of the X-Ray crystallographic data. CasTp server is also one of the easy tools to detect the active sites of the protein.
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