"RMSD from the overall lowest-energy structure" in the HADDOCK 2.4 webserver results page

HADDOCK
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Dear HADDOCK community,

I have a question regarding the “RMSD from the overall lowest-energy structure” provided in the HADDOCK2.4 webserver results page (as average and standard deviation for each cluster).

As far as I can tell, it is different from the i-l-RMSD used for RMSD-based clustering or the i-RMSD and l-RMSD values calculated as part of the CAPRI analysis, is my understanding correct?

If that is the case, what is the definition of this “RMSD value from the overall lowest-energy structure”? In particular, which atoms are used for the superposition and which atoms are used for the RMSD calculation? And is this RMSD the one listed under the column “rmsd_all” in files such as file.nam_rmsd or structures_haddock-sorted.stat in the HADDOCK run structures/it1/water folder?

Thanks in advance for your feedback!

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Dear malfonsoprieto,

Thanks for your interest in using haddock2.4 webserver.

To answer your questions:

  • Yes, the so called “RMSD value from the overall lowest-energy structure” is a Carbon Alpha (CA) rmsd on the all the residues (global rmsd) of the lowest-energy structure. This is because there is no definition of receptor and/or ligand in the current implementation. In the case of DNA/RNA, Phosphate (P) and Carbon (C) atoms are used.
  • Yes, these RMSD values are the ones listed under the rmsd_all header in the files you mentioned.

Of note, if you have the computation power available, please check our haddock3 git repository (GitHub - haddocking/haddock3: Official repo of the modular BioExcel version of HADDOCK), where you can perform a wide variety of rmsd calculations, including: global rmsd, l-rmsd, i-rmsd and i-l-rmsd.

With the hope that this answer helped you.