Error in protein RNA docking

HADDOCK
1

Hello Everyone,

I have to do protein-RNA docking.
I have mentioned the 3 letters code for RNA as:-
A- ADE
C-CYT
G-GUA
U-URA

I am getting following error message:-

There was an error in the processing of the data. Your have been notified by email about the possible cause.

Any help or suggestions to resolve this issue will be highly appreciated.

2

Using the 2.2 web server?

URA should be URI

And did you define the molecule correctly as RNA?

Also it sometimes help to read the PDB in for example PyMol and save it again as PDB format.

3

Thank you for your valuable suggestions.
I think may be problem is with the 3D structure of RNA.
I am new to protein-RNA docking.

How can I predict the reliable 3D model of RNA which can be directly used for protein-RNA docking in HADDOCK.

Thank you in advance

4

Reliable 3D models of RNA is a hard to get… It all depends on the size.
And I can’t really point you to some server for this.

5

RNA modelling is not a trivial task, it will require some experience with modelling methods as well as a good understanding of the RNA molecule itself. The following could be good starting points:

Good luck! :slight_smile:

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