Question: How To Decide Best Docking Conformation From Autodock Results?
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gravatar for Nari
7.4 years ago by
Nari880
United States
Nari880 wrote:

Dear all, I have carried out docking on a protein with a ligand, and obtained result.dlg file with 150 docked conformations.
I have visualized all of them using ADT (Auto Dock Tools).
How to decide which complex is best and how to extract that complex as PDB file.
I am on Windows 7.
Thanks in advance.

docking • 11k views
ADD COMMENTlink modified 4.4 years ago by Arindam Ghosh310 • written 7.4 years ago by Nari880
1
gravatar for quentin.delettre
7.4 years ago by
France
quentin.delettre430 wrote:

First filter/ranking is usually the score of the pose. As the scoring function is a problem by itself for docking protocol, go to second step.

Second is visual/scripting analyzing : if you have a structure of your protein with a ligand, try to check if it is consistent. If not, check that the interactions you see are good.

To get the complex as pdb file, you should read the manual.

ADD COMMENTlink written 7.4 years ago by quentin.delettre430
1

This answer.

Use the scoring function of Autodock. If you can (not sure if Autodock allows that) cluster your solutions and look at the average score of the clusters (or at the average of the top 5 or 10 solutions in each cluster), as this might filter some awkward high scoring isolated solutions.

If you have two clusters or solutions that are close in score, have a look at the structures yourself. Do they make sense? Do they match what they should from the biological role of the protein-ligand complex?

ADD REPLYlink written 7.3 years ago by João Rodrigues2.5k
1
gravatar for Vladimir Chupakhin
7.3 years ago by
Toledo, Spain
Vladimir Chupakhin520 wrote:

For detecting the best docked conformation 1. look for the best 2. use interaction fingerprint for compound known to be active at this target and that do have experimentally derived protein-ligand complex http://www.slideshare.net/chupvl/interaction-fingerprint-1d-encoding-of-3d-proteinligand-information

ADD COMMENTlink written 7.3 years ago by Vladimir Chupakhin520
0
gravatar for Nari
7.4 years ago by
Nari880
United States
Nari880 wrote:

Correct me if I am wrong:

Minimum Binding free energy is possessed by 'conformation No. 112' of all 150.
I extracted the pdbqt form of that ligand conformation and visualized it with protein and then wrote in another pdb together.
Now I have a pdb file with protein and the bound ligand.

Thanks.

ADD COMMENTlink written 7.4 years ago by Nari880

Energy is important, and if you see good interactions (Hbonds, no steric clashes) you can hypothesize than your docking pose is correct.

However, i am not an expert in the field. I just know the basics and you could have learn all that i said by reading the faq of Autodock http://autodock.scripps.edu/faqs-help/faq/what-should-i-look-for-when-i-visualize-a-docked-compound

ADD REPLYlink written 7.4 years ago by quentin.delettre430
0
gravatar for Arindam Ghosh
4.4 years ago by
Arindam Ghosh310
India
Arindam Ghosh310 wrote:

I have a similar problem.... the conformation with the lowest energy has no H-bond but the 4th in terms of energy shows 6 H-bonds. Which conformation should I go for. I am intended to compare the binding of 4 ligands to one protein receptor.

ADD COMMENTlink written 4.4 years ago by Arindam Ghosh310
1

Generally, pose with the lowest docking energy (binding free energy) consider as the best conformation, but you should also check other criteria ; RMSD and the number of interacting residues/ hydrogen bonding, which are very important. The best conformation should follow all these three criteria. And also verify your best pose with other molecular docking tools, Dock6, swissdock, Hex, dock, or Audotock Vina (new version of Audock) etc.

ADD REPLYlink written 4.4 years ago by Mike1.6k
0
gravatar for Arindam Ghosh
4.4 years ago by
Arindam Ghosh310
India
Arindam Ghosh310 wrote:

Also tell me one thing... how do i set the centre for grid box?

ADD COMMENTlink written 4.4 years ago by Arindam Ghosh310
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