Functional form of E_air

HADDOCK
1

Hello all,

I would like to know the functional form of the E_AIR energy term used in HADDOCK scoring. Is it identical to E_NOE that was mentioned in the recent YouTube lectures (bioexcel channel) by Prof. Bonvin ?

Thanks,

2

Yes it is!

1 Like
3

Thanks a lot for confirming.

4

Hello again,

A quick information on the same point:

assign (selection1) (selection2) distance  lower-bound correction  upper-bound correction

If I am right:

L = distance - lower_bound_correction
U = distance + upper_bound_correction

Then how is ā€œSā€ defined in E_NOE ? What are the coefficients of A,B and C? in E_NOE.

Any reference/resource/information would be of help as I could not find this information anywhere.

Thanks,

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5

The original paper is:

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

The value of S used is typically U+2A

1 Like
6

Thanks a lot again for the information.