Molecular Docking Server

PH disabling
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Author:  gosu123 [ Tue Feb 03, 2015 8:13 am ]
Post subject:  PH disabling


I have docked the ligands with both PH disabled and enabled option. However for me the PH disabled option provided better binding pose of the ligand compared to PH enabled option including high binding sore, frequency and so on... what is the major differnce between PH enable and disable during docking. Which one will be the relaible one. Thanks

Author:  bikadi [ Thu Feb 05, 2015 7:51 pm ]
Post subject:  Re: PH disabling

It is not easy to decide in general which is better this is why we offer both option. The microenvironment of a binding site can be very different from a water solution. So pH option can be used to create protonated or deprotonated ligands according to a microenvironment. The better choice is most probably which provides better (e.g. less different binding poses) docking results.

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