Md Simulation Of Protein-Ligand Complex

Question

[dimkal]

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.

Answer 1

[Pappu]

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.

[dimkal]

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?

[Pappu]

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