I have a 30 nucleotide long RNA sequence, the binding of which I wanted to study with a protein (which has crystal structure available). I am trying to model the RNA structure and further use it for docking and simulation. Now, I know a modeled structure of RNA from only sequence without any homologous structure available is not very reliable. But since, I will be doing simulation afterwards can I expect that the near native conformation of the RNA as well as the binding of it to its partner can be studied plausibly ? Kindly help me with some insight.

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