Autonomous University of Tamaulipas
Question
Asked 16th Dec, 2020
What is the best way to find the grid coordinates for docking of a ligand with a protein?
I knew the binding sites in the protein. For docking, Does manually adjusting the grid coordinates is the only option, or are there any tools available to predict?
Most recent answer
DoGSiteScorer tool at https://proteins.plus/ could be helpful.
In this server, you can upload your own PDB file. After DoGSiteScorer execution is completed, you will have the option to download a zip file containing several results. This results can are classified as pockets and residues. The residue files are PDB files containing all the residues in a pocket. This residue file contains the coordinates of the center.
If you are looking for automatization, you could check fpocket (https://github.com/Discngine/fpocket), which also provide the coordinates of the center of the predicted pockets. In both cases you just need to choose the pockets than correspond to the binding sites of the protein and look for the line with the coordinates.
All Answers (4)
German Cancer Research Center
Hi Madhu,
If I am correct, It seems you are asking two questions:
1) You want to predict the binding site
2) You know the binding site and you want to create a grid around it.
If you want to predict, then follow this:
(This won't give out X, Y, Z coordinates. Only amino acid residues of the pocket)
2) If you have Schrodinger, then use Sitemap
and, if you already know the binding site, just make the grid big enough manually.
It shouldn't be a problem.
Hope it helps!
1 Recommendation
Airlangga University
Hi Madhu,
if you want to find the coordinate of the binding site that already know.
Dependent on which docking software you use cause diferrent software will give different procedural but, the point is same for calculation needed.
I recommend to use DOCK6 cause it have tools sphere selection and grid function scoring to find the active site based on native ligand coordinate. You can find the toturial in here:
Hope it helps
1 Recommendation
Autonomous University of Tamaulipas
DoGSiteScorer tool at https://proteins.plus/ could be helpful.
In this server, you can upload your own PDB file. After DoGSiteScorer execution is completed, you will have the option to download a zip file containing several results. This results can are classified as pockets and residues. The residue files are PDB files containing all the residues in a pocket. This residue file contains the coordinates of the center.
If you are looking for automatization, you could check fpocket (https://github.com/Discngine/fpocket), which also provide the coordinates of the center of the predicted pockets. In both cases you just need to choose the pockets than correspond to the binding sites of the protein and look for the line with the coordinates.
Similar questions and discussions
How we can get the (binding site coordinates) from (Binding Site Residue)?
How we can get the (binding site coordinates) from (Binding Site Residue)?
Accully, schrodinger (Glide) users use (Binding Site Residue), but this feature in not available in Autodock vina.
Example:
Predicted Binding Residues :7:A 8:A 9:A 16:A
I need to get the (x,y,z) of this residues.
Note:
(RESIDUE DEPTH) is example of aplication for predictting residuse http://cospi.iiserpune.ac.in/depth/htdocs/run_depth.html
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