How can I dock a protein to a nucleic acid?

Question

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?

You mean a specific RNA molecule, right? Not any RNA in general? — terdon, Jun 27 '17 at 18:00
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. — Joe Healey, Jun 27 '17 at 18:19

score 3 · Accepted Answer · edited Jun 28 '17 at 09:05

3

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.

edited Jun 28 '17 at 09:05

llrs

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answered Jun 27 '17 at 23:24

Marcin Magnus

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How can I dock a protein to a nucleic acid?

1 Answers1