Question: Molecular Docking With Gold - How To Define A Ligand Binding Site?
7
gravatar for Pals
8.8 years ago by
Pals1.3k
Finland
Pals1.3k wrote:

I have been using the latest version of GOLD for docking ligand (Sugar substrate, GDP-Man) to the binding site of protein structure. After the docking process is completed, ligand is docked in the right place but the problem is that the conformations are inverted. The part that should be in acceptor site is seen in donor site and vice versa. It is not always the case, some of them are in right orientation and some are in wrong. Now, in that case, is there any way to define particular site to be in particular place so that every docked ligand would be in right orientation? I had heard some time that we can define such sites but I have not yet been able to do it. Actually I am using GOLD within Discovery Studio 3.0. If this option is not available or this operation is not possible with GOLD, could you suggest another docking program which would provide better results.

Thanking you in advance!

docking • 5.6k views
ADD COMMENTlink modified 5.7 years ago by Biostar ♦♦ 20 • written 8.8 years ago by Pals1.3k
1
gravatar for Pals
8.8 years ago by
Pals1.3k
Finland
Pals1.3k wrote:

Thank you chupvl for the suggestions. However, as I have three different proteins among which two are having nice poses even without constraints, I wanted to improve those two and define constraints for the one that had bad poses. I prefered to use GOLD, the default program instead of some other programs. My supervisor suggested and recommended to find such options. She had experience of using standalone GOLD for docking but as she did not have experience of using GOLD within Discovery Studio, I had to find myself. Now I have managed to find the right manner to restrict interaction site as well as define particular atom in the ligand to interact with particular atom in the substrate. I defined the interaction site with a "define and edit binding site" and I found yet another tool that defines constraints based on ligand structure where I can restrict a particular atom or group to interact with particular atom or group of substrate using "constraints input scaffolds" parameter.

ADD COMMENTlink written 8.8 years ago by Pals1.3k
1

GOLD do have constrain docking features: (a) you can provide atoms of the protein and ligand (b) just the H-bond for the protein More details about constraints here - http://www.ccdc.cam.ac.uk/support/documentation/gold/5_0/gold_conf/gold_conf.1.6.html

ADD REPLYlink written 8.6 years ago by Vladimir Chupakhin520
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