Hello everyone,
I tried to dock a ligand to a molecule using AutoDock software with a blind docking method. My ligand is an under-investigated small-drug molecule and the protein interactions of the ligand is not known. From my docking results the binding energy for the molecules I investigated was found as -5.78, however there was no hydrogen bonds formed between these molecules. Can I assume that these molecules are docked or how can I check the reason why hydrogen bonds weren't formed?
Additionally, is there any way anyone can recommend to screen the proteins interacted with a ligand whose proteins interactions weren't studied?
Sorry for the inconvenience,
Thanks in advance.
Mervenur
There are mutliple known complexes where binding of the ligand is strong and there are no hydrogen bonds. There are many types of other, van der Waals interactions, that provide quite strong interaction energies. So the lack of any hydrogen bonds does not automatically mean that you pose is wrong. Take a look at the structure of the binding site and ligand - perhaps there are no good candidates for hydrogen bonds? Obviously you may also want to rerun the docking in a more complete manner, use different docking algorithms/programs for comparison and so on...
Why have you decided to dock the compound to that particular protein? What is your definition of hydrogen bond? What is the source of the protein -- experimental structure or homology model? Is the binding site complementary in charge and shape to the ligand? Is the binding site "druggable"? Do you have access to molecular biology lab to validate your docking hypothesis by site-directed mutagenesis?
Instead of blind docking: identify pockets, e.g. using DoGSiteScorer (https://proteins.plus/), and dock into them. And search PDB for proteins with similar pockets, e.g. using SIENA (also at Proteins+), and if you find any, check if they contain ligand.
Hello Martin,
I have decided to dock the compound to that particular protein, because in our lab, we generated a proteomic data from compound-treated cells and I randomly selected a few of them which found to be differentially expressed compared to control ones. I extracted the pdb format of the protein from the Protein Data Bank. I don't know if the binding site druggable I am very new at this docking studies how can I check?
Thanks.
Hi mervenur
Please paste the coordination of the best pose of docked molecule to the pdb structure of protein (without water molecules) and open it BIOVA discovey studio Visualizer. It can be downloaded from following address:
https://discover.3ds.com/discovery-studio-visualizer-download
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