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.
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.
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
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.
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
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.
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.
Also tell me one thing... how do i set the centre for grid box?
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version 2.3.6
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?