Question: Docking Problem
2
gravatar for Spandankeshav
8.2 years ago by
Spandankeshav160
Turku, Finland
Spandankeshav160 wrote:

Hello there,

I am trying to do dock by the use of GOLD through Discovery Studio. I successfully run the GOLD operation but unfortunately I couldn't get a single dock (0 poses). I tried to do it several times by changing the different parameters available and also by adjusting GOLD's default parameters as well. Actually, I prepared protein and ligand (both) well before submitting the job (added all hydrogen atoms) and also the receptor site in protein by creating well sphere around the ligand binding site. However, the result's were all the same. But when I tried to do same job by using SOMA2 (which is available in CSC) with same selection of atom as in Discovery Studio I was able to get docking results. I am wondering why couldn't get any doc poses while using DS (GOLD)...any suggestions please?

PS: All the suggestions and help will be highly appreciated!

Cheers! Spandan

docking • 2.7k views
ADD COMMENTlink modified 6.6 years ago by Biostar ♦♦ 20 • written 8.2 years ago by Spandankeshav160
1

It will be diffucult to help without any provided details. Did you took a look at the GOLD log file?

ADD REPLYlink written 8.2 years ago by Vladimir Chupakhin520

This. Give some more information on the log file otherwise our suggestions will be blind..

ADD REPLYlink written 6.6 years ago by João Rodrigues2.5k

GOLD is based on genetic algorithm, which starts with random population. so Each GA run will give different result. In your binding site, if some of the residues were clashing with your ligand, then in the initial screening off GOLD, these poses will be elliminated. So you could do one thing,

The docked complex that you got by using SOMA2, u just relax or minimize and then take the complex as starting structure for input to GOLD. Definitely the ligand can now fit well in the ligand binding site.

ADD REPLYlink written 8.2 years ago by Priyabrata0

Thanks for the reply but I couldn't get what you want to say. You mean, that complex which I got after gold docking could be used for the initial parameter for another docking?? I mean those docked ligands that I got after first dock??

ADD REPLYlink written 8.2 years ago by Spandankeshav160
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