Hello there,
I have attempted a docking Study using Auto dock vina, the results were quite logical and interpretable, yet I wanted to refine them due to high RMSD values, and I wanted a way to quantify enzyme inhibition through IC50. I have though about using Auto dock (not vina) but the process of binding pocket setting seems hectic to me especially that the protein am using has 2 binding pockets and I want to investigate them both. So I though about using MOE, running a preliminary docking, the results didn't correlate with the one I had from vina and the RMSD values were too high.
So I need some insight on.
Which is the most suitable algorithm to use in MOE, if not how to know what suits me the best.
How to investigate two binding pockets (site finder not able to distinguish them clearly)
Can i use MOE Qsar and create my own model to quantify inhibition
In MOE you can change the parameters to broadly define a bigger binding site. Alternatively you can add manually or with the selection/extend tool more residues. To have better docking results try to define a bigger binding site, and also try energy minimization as second refinement step, having a big number of retained structures in the first refinement.
Arturo Rojo Sir, can you explain more details about the term "try energy minimization as second refinement step, having a big number of retained structures in the first refinement"?
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