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PostPosted: Sat May 17, 2014 2:59 pm 
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Joined: Sat May 17, 2014 2:47 pm
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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

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