# RNA-protein blind docking active residues question

**URL:** <https://ask.bioexcel.eu/t/rna-protein-blind-docking-active-residues-question/3987>\
**Category:** HADDOCK\
**Created:** [November 13, 2022, 10:37pm UTC](https://ask.bioexcel.eu/t/rna-protein-blind-docking-active-residues-question/3987 "2022-11-13T22:37:10Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![h4dd0ck\_RNA](https://avatars.discourse-cdn.com/v4/letter/h/ecae2f/32.png) [@h4dd0ck\_RNA](https://ask.bioexcel.eu/u/h4dd0ck_RNA)\
**Post date:** [November 13, 2022, 10:37pm UTC](https://ask.bioexcel.eu/t/rna-protein-blind-docking-active-residues-question/3987/1 "2022-11-13T22:37:10Z")

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Hi All,

There is a known PDB structure I am using that has solved a NMR structure of a RNA-Protein interaction. I am trying to replicate this ( to test HADDOCK parameters) by submitting just the protein chain as my protein ligand, and submitted a computed 3D structure of the RNA using online folding.

I find that the resulting structure is not identical to the NMR-solved structure and am wondering on how to refine my model further. I know the active residues based on the known structure but right now, I am not designing specific residues as active - I wanted the docking program to compute the residue interaction but I cannot set both the RNA and protein as passive, so I have instead highlighted all RNA and protein residues as active. Is this acceptable, and if not, how would I proceed to theoretically dock my RNA/protein without biasing the model by selecting interactive pairs of residues/nucleotides?

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**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\
**Post date:** [November 14, 2022, 7:47am UTC](https://ask.bioexcel.eu/t/rna-protein-blind-docking-active-residues-question/3987/2 "2022-11-14T07:47:33Z")

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An Initio protein-RNA docking is not trivial

In Haddock better use in that case the center of mass AB initio mode (does require expert level access), increase the sampling (e.g. 10000/400/400) and set all desolvation energy weights to in the scoring function