First, I did a blind docking to my protein since I do not know its binding site. Then I noticed certain clusters of ligand conformations. The lowest energy conformation binded to a different site while the rest binded to other sites. One of the sites have 5 conformations in it and I took this site for another docking calculation even if it is not the site where the conformation of the lowest energy binds and taken into account the number of the conformers in the site. Is this process valid?
Ren Vien Anthony Fernandez,
Have you taken into account the size of docked ligands?
Hi Mohsin Yousuf Lone, I have only one type of ligand used in the docking. So all of the conformers basically has the same size. Can you please elaborate the effect of ligand size and how can it influence the process I have mentioned in my question?
Usually a increased probability can be reinterpreted as more energetically favorable, at least from real molecular dynamics simualations. If you do not know where the binding of our ligand acually occurs, I'd recommend doing MD first, for handful of times and see where the ligands end. This would also include induced conformational changes to the protein and the ligand in the course of binding and might therefore point out why the docking gave such inconsistent results. Different binding positions of the ligand could also compared by other MD methods such as mmgbsa or FEP.
You can also try our Blind Docking server:
http://bio-hpc.ucam.edu/aquiles/
Achilles Blind Docking server at:
https://bio-hpc.ucam.edu/achilles/
In order to find more information and for discussion I suggest you to join the Structural Bioinformatics and High Performance Computing (BIO-HPC) discord server at:
https://discord.gg/fZyNYTsT7k
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