Question: Docking With Two Substrates
gravatar for Elmo
7.9 years ago by
Elmo130 wrote:


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 • 1.8k views
ADD COMMENTlink modified 7.9 years ago • written 7.9 years ago by Elmo130

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

ADD REPLYlink written 7.9 years ago by ancient_learner630

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 7.9 years ago by Elmo130

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 7.9 years ago by ancient_learner630
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2117 users visited in the last hour