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Md Simulation Of Protein-Ligand Complex

Dear all, please tell me what type of analysis do you find useful after running MD simulations of a protein-ligand complex. I'm developing a tool that characterizes interactions between a protein and a ligand and I'm looking for ideas on different types of analysis. If you can provide a link to an article with an example it'll be great.

simulation
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updated by Biostar Biostar • written by dimkal dimkal

1 answer

Any kind of analysis can be performed on MD trajectories. The first thing, I would look is the change in RMSD of the complex in order to find out if it is stable. You can have a look at gromacs analysis tools and related for more analysis options.

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written by Pappu Pappu

so you look at RMSD and you see that converged to some value, what would be your next steps? You know the ligand; and the residues that come in contact with it throughout the trajectory, what would you want to do with this information?

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written by dimkal dimkal

J Chem Inf Modeling has many papers on this area. Look what people usually do for what purpose. What is your objective?

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written by Pappu Pappu

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