i have one protein with two different active sites and normally hydrolyzed by two different chemical compounds in the human body in normal condition.
so question is that can i dock this with two analogy of normal compounds by using Audodock 4.2
There is a procedure called multiple ligand simultaneous docking described in the paper found at this link in PubMed:
https://www.ncbi.nlm.nih.gov/pubmed/26414950
It is also possible to do sequential docking. In this procedure, the first ligand is docked and the complex is saved out as a single file, where the first ligand is considered part of the receptor. Docking is then carried out on this complex with the second ligand.
You need to define two different grid box for these two active sites. Run the program for them separately.
Hi Vinod Kumar Jatav,
It is possible that an enzyme can have multiple binding sites for different substrates. MLSD can be employed for a competitive binding of multiple substrates at a single binding site. If the binding sites are different multiple binding sites can not be defined in AutoDock for a single run.
If the binding and its effect is independent for two ligands, then you can either dock them one after the other as detailed by Dr. Rudy J Richardson above or you can independently run irrespective to one another.
All the best
Sure,
MLSD procedure is mentioned in the article link given by Dr. Rudy J Richardson above. But I doubt (please correct me if I am wrong) it is applicable in your case since both the molecules binds at different binding sites.
For consecutive docking you can dock first molecule and then you can save the minimum binding energy pose as a complex in .pdb format. Then you can use that complex to dock the second molecule. since two molecules bind at different binding sites, they will not interfere with one another.
Dear Aditya Rao, do you have a step by step procedure to do MLSD for different sites in a same protein or vice versa? most of the papers dont exactly say what has to be done with AUTODOCK to do MLSD.
Sanjay KUMAR Palayat Hello. I am also stuck with the same problem. Did you find an answer to this problem or have you found an alternate?
Can you please share your views?
Will be really helpful.
Thanks.
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