I am trying to find an inhibitor for a protein, and for that purpose, I did preliminary docking using Autodock to find potential inhibitors. Now, I need to check if that docking is stable or not. What I have found from few literatures that this can be done in two ways: either I get the docked complex, and do the MD simulation, OR, I get spectrum of protein structure using MD simulation, and repeat the docking and take the average and match with initial value to find both values are not very different. Please explain what should I do in my case, and how to do that? I know about the docking part, but not sure about the MD simulation part as I am quite new to this area. And also, please let me know if I need to explain my question a bit more.
Hi,
I hope i am not too late with the answer. Performing MD simulation after docking is a good way to validate your docking studies. Both the suggestions from the literature you found seems plausible. But i would go with the first one. Build the complex with your protein and docked inhibitor , then perform MD simulation for the complex using Gromacs.
Since you are new, gromacs is a nice way to start. You can find how to perform simulation using gromacs in the below link.
http://www.mdtutorials.com/gmx/complex/
After simulation,you can perform wide range of analysis including RMSD, binding energy calculation (g_mmpbsa), interaction studies during the course of your simulation time.
Thanks for the comment Keerthic Aswin. I did use GROMACS, and everything seems to be working fine. I am just RMSD study to confirm that, but I can only RMSD value of the whole complex, and in literature, I have seen people do both free as well complex form study, and report both the graphs together. Can you tell me how to do a free protein RMSD study? Do I have to start from the very beginning or have to change something during the rmsd calculation? Thanks in advance!
Hi Adarsh Singh ,
For free protein RMSD, you have to start a new simulation with protein alone as the binding of inhibitor brings changes in the residue network of protein. Iin case, you want to understand structural changes in your protein of interest upon inhibitor binding. you can do additional simulation with protein alone and then perform analysis (RMSD, Rg etc) on both of them to compare between bound and unbound state of the protein. This kind of comparison can help you find out the stability of your protein upon binding docked inhibitors ( i guess that's what you want to study).
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