I have a protein of interest and I would like to now how it interacts with RNA. I have structures of both molecules.
What tool can I use?
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I'm not sure what you meant but you can take a look at NPDock (disclaimer we wrote that tool). If you have a structure of your protein of interest, you can dock it to the structure of your DNA/RNA of interest. Mind that this is a rigid body docking which means that the structure will not change upon binding.