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Vina docking poses vs x-ray (symmetry problems)
http://mgl.scripps.edu/forum/viewtopic.php?f=12&t=3360
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Author:  dudak [ Sat Jan 07, 2017 10:12 pm ]
Post subject:  Vina docking poses vs x-ray (symmetry problems)

My name is dudak. Hi all
We are trying to dock a small set of ligands in to a protein structure

when docking the x-ray ligand to its protein we obtain an inversed ligand into the active site. the xray pose can be found in the 9 generated poses but never be the best conformation.

based on x-ray structure we caracterized the ligand-receptor interaction and we cannot obtain the bioactive conformation in the first model. it is always the symmetrical conformation that we obtain. this is true for a set of ligands that share some the same scaffold with the x-ray ligand.

The active site is composed from 2 hydrophobic pockets and the ligands have in both extremities benzene cycles. can this impact the docking poses.
protein and ligands have been prepared and pdbqt structures obtained with the newest MGL tools. exhaustivness has been set to 100 with a box of 15x15x15.

can any body help us with this symmetry problem ???.
Thanks in advance

Author:  Sophie [ Mon Jul 31, 2017 11:55 am ]
Post subject:  Re: Vina docking poses vs x-ray (symmetry problems)

I'm also interested, although judging by the past time, I do not think that you will get an answer here) If somewhere on another resource will help you, let me know, I will periodically check pm.

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