Hi everyone. So I have performed MD simulations on desmond of my protein bound to a mutant peptide? My objective is to elaborate how the mutant peptide is inducing conformational changes in the protein. How to answer the above question by looking at the RMSD? How can I explain the given RMSD in detail?
Ayesha Fatima
Hello Alina
You can begin by looking at the change in structure over time and comparing g it with changes in your RMSD. Where ever there is a drastic jump or dip in the RMSD, you have see what are the changes especially where the mutation was introduced and compare with the wild type.
You can look at the bonding behavior of the mutant and the wild type also.
I hope this helps
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