How is Eair calculated?

HADDOCK
1

Hi!

I would like to know where to find a detailed information about how the restraint violation energy (Eair) of a docking is calculated; the way how a violation of a unambiguous restraint or ambiguous is weighed mainly.

Thanks in advance

2

This goes back to the 2003 original JACS paper. And the restraining energy function is actually the one described in Eq. 8 of:

Nilges, M. (1993). A calculation strategy for the structure determination of symmetric dimers by 1H NMR. Proteins: Structure, Function, and Bioinformatics, 17(3), 297–309. http://doi.org/10.1002/prot.340170307

Screenshot 2023-01-26 at 19.28.36
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And in the restraining function, r=deff

3

Thank you for the detailed and helpful answer. I would like to know too how unambiguous restraints (for example from XL-MS data) are incorporated in the restraining function.

thanks in advance

4

Same as AIRs in principle. It is the same energy function used.

The atom selection in the restraint will define how many atoms are considered when assessing the 1/r**6 sum.
If the XL-MS restraint is specific to two atoms, it will be simple the distance between those.

5

Hi,
Are A, B, and S constants? or depend on the restraint distance?
Thank you

6

These are indeed constants and do not depend on the distance