In my opinion you should remove the reference ligand and then dock the protein in the same binding site as that of reference ligand....

Hi Madhav Agarwal,

If i remove the reference ligand, how can i find that binding site for docking?? 

You can find the active site using the servers like CastP,metapocket etc....but do remember that your active site must contain the residues from which your reference ligand binds....

Thank You for your valuable comments Mayank Agarwal. I am planning to do it in that way .

Hi

In my perspective its better that you find residues that have interaction with your reference ligand, then after minimization you must set active site geometry  by finding these residues.

best regards.

Hi,

Using Discovery studio visualizer you can find the binding site residues of the reference ligand and then you can use same residues as a binding site to your experimental ligands, other way can be like predict the binding site using servers mentioned by Mayank Agarwal. Hope this helps.

Regards

Danish Jasnaik,

I tried "DoGSiteScorer: Active Site Prediction and Analysis Server"for finding out the active site around the reference ligand. 

When I checked the interacting molecules of reference ligand using Discovery Studio Visualizar, all interacted molecules were present in the predicted site . 

But a Small problem what i found was size of active site was a bit larger and contains a few more amino acids

Mohamad Akbari

Do we need to take  only that interacting residues as active site or do we need to consider the other aminoacids around it?

Dear Sajin

Its depend on your software that used. for example in Autodock try to set grid box a bit larger than your amino acids space. because if you set large box your result won't be reproducible.

Dear Mohamad Akbari

Am using arguslab for docking. 

In argus lab we can select the  aminoacids and we can prepare it as binding site. !!

Hi: better use free Autodock Vina allowing the use of flexible residues at the binding site.

If your are trying to define binding sites of ligand on viral envelope proteins, then it is better to perform energy minimization along with the reference ligand or experiment ligand. Energy minimization without ligand may give a better structure of envelope protein which may not be suitable for your ligand docking. Having a reference ligand with envelope glycoprotein structure will allow you to energy minimize the the structure with respect tothe lignad interaction to the envelope protein.!!!!