Question: Docking With Two Substrates
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gravatar for Elmo
6.1 years ago by
Elmo110
Elmo110 wrote:

Hi,

I have some doubts on Docking. I have modeled out a structure from homology modeling and perform some refinement. Now, there are two substrates to be introduced to the protein structure. The protein that I am studying is an enzyme and it catalyzes the reaction of two substrates. I have read about docking with one substrate / ligand, but not with two. How can I possibly do that? Any article references or advice please?

Thanking you in advance.

Best regards, Elmo

modeling homology docking • 1.5k views
ADD COMMENTlink modified 6.1 years ago • written 6.1 years ago by Elmo110

If you are using softwares like schrodinger (maestro) you can dock as many ligands as you want at a time

ADD REPLYlink written 6.1 years ago by ancient_learner610

Hi @anurupadevi, thanks for replying. My enzyme protein has a catalytic triad that when one substrate binds to it, only then the other substrate can bind to it. I was wondering if I should dock one substrate first, and then run some simulation and then only introduce the other substrate, or should I introduce both and then only do simulation? Please advice. Thank you.

ADD REPLYlink written 6.1 years ago by Elmo110

If the binding of one substrate brings conformational change to the protein that accommodates the other substrate, Yes i think you have to go with simulation after the docking of first substrate.

ADD REPLYlink written 6.1 years ago by ancient_learner610
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