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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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    $\begingroup$ You mean a specific RNA molecule, right? Not any RNA in general? $\endgroup$
    – terdon ♦
    Commented Jun 27, 2017 at 18:00
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    $\begingroup$ Autodock Vina is a common tool for ligand binding studies, if the stretch of RNA isn't too large I suspect it may work with Vina. $\endgroup$
    – Joe Healey
    Commented Jun 27, 2017 at 18:19

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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.

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