How is Eair calculated?


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

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.

And in the restraining function, r=deff

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

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.