Molecular Docking Server

How to target only the active site?
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Author:  dockguest [ Wed Jun 24, 2009 12:26 pm ]
Post subject:  How to target only the active site?


I would like to tell to the ligand to search for binding in a preselected area (active site) of the protein target and not in the whole protein ....How to do this?

More,is it possible to search for active sites? :?: :?:

Author:  hazaie [ Wed Jun 24, 2009 3:22 pm ]
Post subject:  Re: How to target only the active site?

At the select protein box step you can set up the size and the coordinates (center) of the simulation box. This simulation box defines the search space for docking caclulation. So all you need to do is to set the simulation box to the active site. It should be noted that by clicking on the ligand name in the sequence (after selecting the checkbox for "Show sequence") the simulation box will be centered on the bound ligand automatically.

If you choose the whole protein as atarget that will search for poteintial binding site.

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