Weights Used in Computing the HADDOCK Score

HADDOCK
1

Hello,

I am using HADDOCK for peptide-protein complexes and found that the weights used to calculate the HADDOCK score are the following:

HADDOCK-score it0 = 0.01Evdw + 1.0Eelec + 1.0Edesolv + 0.01Eair - 0.01BSA
HADDOCK-score it1 = 1.0Evdw + 1.0Eelec + 1.0Edesolv + 0.1Eair - 0.01BSA
HADDOCK-score itw = 1.0Evdw + 0.2Eelec + 1.0Edesolv + 0.1Eair

May I ask how these weights were obtained and why they would differ in each stage of docking? For the empirical terms like BSA, why must it be subtracted from the score in the first two and not in the last stage?

Any reference paper discussing this for peptide-protein docking with HADDOCK would greatly help as well. So far, I’ve been reading the one by Vangone et al., 2016 but couldn’t find what I was looking for.

Thanks a bunch!

2

You need to go back to the original JACS 2003 paper.

Different scores at different stages because the protocol and setting of those are different.

Further the more negative the score the better.

Evdw and Eelec can be and should be negative values, while BSA is always a positive term, which is way we give it a negative sign to select for large buried surface areas.

The protein-peptide weights are the same as the protein-protein ones.