# RMSD of docked proteins vs co-crystallized structure from PDB

**URL:** <https://ask.bioexcel.eu/t/rmsd-of-docked-proteins-vs-co-crystallized-structure-from-pdb/5873>\
**Category:** Uncategorized\
**Created:** [September 1, 2025, 12:32pm UTC](https://ask.bioexcel.eu/t/rmsd-of-docked-proteins-vs-co-crystallized-structure-from-pdb/5873 "2025-09-01T12:32:14Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![Eugeneng991031](https://avatars.discourse-cdn.com/v4/letter/e/8dc957/32.png) [@Eugeneng991031](https://ask.bioexcel.eu/u/Eugeneng991031)\
**Post date:** [September 1, 2025, 12:32pm UTC](https://ask.bioexcel.eu/t/rmsd-of-docked-proteins-vs-co-crystallized-structure-from-pdb/5873/1 "2025-09-01T12:32:14Z")

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Hi , I was just wondering if it’s realistic enough to get the docked protein’s RMSD value close to 0 when compared to Co-crystallized structure? I know that will be the ideal structure but practically is it achievable? If not, what are the RMSD value that are consider good enough for further analysis ?

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**Author:** ![AKravchenko](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/akravchenko/32/1168_2.png) [@AKravchenko](https://ask.bioexcel.eu/u/AKravchenko)\
**Post date:** [September 1, 2025, 1:15pm UTC](https://ask.bioexcel.eu/t/rmsd-of-docked-proteins-vs-co-crystallized-structure-from-pdb/5873/2 "2025-09-01T13:15:39Z")

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Hi, never tried this myself, but in principle, this should be achievable for the backbone RMSD - if one performs bound docking with unambiguous restraints. Also, this is likely to depend on the experimental structure itself - it may be more or less optimised, it may have not-great resolution, etc.  
Thus, sometimes people use an energy-minimised experimental structure as a reference instead of the original coordinates that have been deposited on PDB.

For real-life protein-protein docking, one option is to use CAPRI metrics:

- acceptable model: i-RMSD \< 4Å or l-RMSD \< 10Å and Fnat \> 0.1 (0.23 \< DOCKQ \< 0.49)
- medium quality model: i-RMSD \< 2Å or l-RMSD \< 5Å and Fnat \> 0.3 (0.49 \< DOCKQ \< 0.8)
- high quality model: i-RMSD \< 1Å or l-RMSD \< 1Å and Fnat \> 0.5 (DOCKQ \> 0.8)

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**Author:** ![Eugeneng991031](https://avatars.discourse-cdn.com/v4/letter/e/8dc957/32.png) [@Eugeneng991031](https://ask.bioexcel.eu/u/Eugeneng991031)\
**Post date:** [September 1, 2025, 11:56pm UTC](https://ask.bioexcel.eu/t/rmsd-of-docked-proteins-vs-co-crystallized-structure-from-pdb/5873/3 "2025-09-01T23:56:39Z")

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Good day. Thanks for the reply, yes unambiguous restraint may lead to a lower RMSD. However, my group leader may argue that over restraining the protein interaction may not be natural enough.

Anyway, is there a way to determine the I-RMSD or FNAT ? As so far I had been using ChimeraX as my molecular viewer and the RMSD there I suspect it to be backbone RMSD

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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:** [September 2, 2025, 7:02am UTC](https://ask.bioexcel.eu/t/rmsd-of-docked-proteins-vs-co-crystallized-structure-from-pdb/5873/4 "2025-09-02T07:02:43Z")

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You could use the CAPRI-Q resources for CAPRI metrics assessment:

The source code is freely available from [CMSB-public / CAPRI-Q · GitLab](https://gitlab.in2p3.fr/cmsb-public/CAPRI-Q)

and its web interface through the Dockground resource at [Dockground - Assessment](https://dockground.compbio.ku.edu/assessment/)

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**Author:** ![Eugeneng991031](https://avatars.discourse-cdn.com/v4/letter/e/8dc957/32.png) [@Eugeneng991031](https://ask.bioexcel.eu/u/Eugeneng991031)\
**Post date:** [September 3, 2025, 1:02am UTC](https://ask.bioexcel.eu/t/rmsd-of-docked-proteins-vs-co-crystallized-structure-from-pdb/5873/5 "2025-09-03T01:02:08Z")

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Thanks Prof, you are a lifesaver 🥹