Water refinement HADDOCK2.2: data interpretation

HADDOCK
1

I have a question regarding results after water refinement performed using Multi-body interface of Haddock2.2 and the following recipe: Advanced refinement of molecular complexes – Bonvin Lab

I was introducing single mutations into an initial structure of a trimeric protein one by one and then comparing the refined variants according to the resulting energetic scores. Many of the mutated residues are located further than 5 Å from the chain interfaces. And here are my questions:

  1. As I understand now, by default only the interchain energetics are calculated, (including only the residues 5 Å around the interfaces) and therefore the resulting score includes only the energetic contribution of those residues. Is this correct and if not, then contribution of all residues is included?

  2. If the first assumption is right and only energetic contribution of the residues from the interface are included into the final score, then the score of the introduced mutation of a residue beyond 5 Å of the interface is not influenced by the mutation?

Thank you for your time.
Best regards,
Marija

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  1. the score includes all intermolecular interactions, but the non bonded energies are truncated at 7.5A. Meaning any pair of atoms at a distance larger than 7.5 will contribute 0 energy
  2. They might still impact the interface during the flexible refinement, even if they don’t contribute to the score directly at the end (if they don’t have intermolecular interactions within the 7.5A above cutoff). And during the refinement all interactions are considered (both intra and inter)
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Thank you for your prompt reply. I am still a bit confused about a few things:

I was performing only structure refinement, so that means that all non-bonded interactions (intra- and inter-molecular) are calculated for all pairs of atoms within 7.5 Å around the interface. But if for example two atoms of the same molecule interacts via H-bond, but one atom is within 7.5 Å of the interface and the other one above the threshold, would this interaction still contribute to the final score, or it will have also 0 energy?

Or for refinement contributions of non-bonded interactions between each atom with all other atoms 7.5 A around it are calculated, independently of their distance from the intermolecular interface?

Thank you for your patience.

4

For the score all intermolecular atom-atom interactions with a distance shorter than 7.5A are calculated (I.e. more your second point).

Basically all intermolecular interactions are considered but only those with a distance shorter or equal to 7.5A will have a non zero energy

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