Nucleic acids docking

Dear HADDOCK admins and users,

I am checking RNA docking via Haddock. I have a miRNA structure including a 5’-phosphate cap that I would like to bind it with an mRNA structure.

This phosphate gives me the error : “Instances of ligand U do not contain the same atoms” since there is a difference in comparison with the other present U bases in the PDB file.

Should I just omit this atom? Is there any preferred procedure for Haddock specifically? (I have a similar problem with Gromacs by the way but I expect the procedure to be related.)

Thanks in advance.

Kind regards,

First make sure to use a three letter code for the bases

Are you submitting an ensemble or a single model?

Hello mr. Bonvin,

Firstly, thank you for Haddock.

I see, a three letter code is needed. I will make the change and I will give it a try.

They are single separate models, not ensembles.

Update: I changed the residue names to three letter codes (U -> URI, G -> GUA, A -> ADE, C -> CYT) and the problem was resolved. I chose the bases of both RNAs but I got an unexpected docking result. Maybe the passive residues setting is related to this. I will experiment with this more. Thank you.

Is there any way to specify pairs of active residues or the binding sites explicitly? The resulting docking is not focused on base pairs. Maybe I need to use a more advanced interface?

You can customise your restraints as you wish. For this you need indeed access to the expert interface.

If base-specific, then the restraints should be targeted more to the base and not the ribose.
The syntax for restraints follows the CNS syntax and it very powerful.

Check for examples Box 4 of our our Nature Protocols 2010 server paper:
The HADDOCK web server for data-driven biomolecular docking. Nature Protocols, 5, 883-897 (2010). Download the final author version here.