Can the haddock be used to tackle the RNA-RNA systems?


The HADDOCK category is meant to discuss any HADDOCK-related issue. For general information about HADDOCK refer to

I have two RNAs and they may have some interactive points determined by ITC. So, I want to model the RNA complexes by haddock. Does that make sense? If do, how can I specify the base pair interaction between them(in the docking, for example: between A: 14G 15C 16A and B: 33U 34G 35C)?


Dear Yikan,

In principle it can be done. Simply specify RNA as molecule and make sure you are using a 3 letter code for the residue names.

To learn how to define restraints in CNS format (or define active residues), please check our tutorials and/or refer to our Nature Protocol 2010 paper where we provide examples