Question

Asked 3rd May, 2019

Pontificia Universidad Javeriana

How can I properly stablish the size of the grid for a docking in AutoDock Vina?

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?

Patna Women’s College

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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Horacio Pérez-Sánchez

Universidad Católica San Antonio de Murcia

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

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5 Recommendations

Yoshinobu Ishikawa

Shonan University of Medical Sciences

Annemarie Honegger

University of Zurich

Uttam Pal

S.N. Bose National Centre for Basic Sciences

Martin Klvana

Rudy J Richardson

University of Michigan

i remembered i had used an algorithm which can cluster different binding site as predicted from different sites. however as suggested by Suresh Kumar , his answer is really good. However, do not go for blind docking or do not consider whole receptor as a grid, the result would be most likely false positive .

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1 Recommendation

Horacio Pérez-Sánchez

Universidad Católica San Antonio de Murcia

https://www.nature.com/articles/s41589-019-0278-6

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5 Recommendations

Jairo Enrique Mercado

Universidad de Cartagena

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.

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1 Recommendation

Bakary Ntji Diallo

Rhodes University

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...

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Arti Kumari

Patna Women’s College

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What is the default grid spacing in AutoDock Vina?

Question

4 answers

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10 answers

Asked 7th Mar, 2016

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Question

1 answer

Asked 8th Feb, 2023

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Question

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Question

7 answers

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