# Binding energy of docked complex

**URL:** <https://ask.bioexcel.eu/t/binding-energy-of-docked-complex/3299>\
**Category:** HADDOCK\
**Created:** [October 15, 2021, 9:52am UTC](https://ask.bioexcel.eu/t/binding-energy-of-docked-complex/3299 "2021-10-15T09:52:07Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![valentino](https://avatars.discourse-cdn.com/v4/letter/v/6bbea6/32.png) [@valentino](https://ask.bioexcel.eu/u/valentino)\
**Post date:** [October 15, 2021, 9:52am UTC](https://ask.bioexcel.eu/t/binding-energy-of-docked-complex/3299/1 "2021-10-15T09:52:08Z")

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Hello, I would like to compute the interaction energy between two proteins docked with haddock.  
I see that each cluster pdb contain the terms: Binding Energy, Desolvation Energy and Internal Energy of isolated and docked molecules.  
Although I get haddock score \< -2, the binding energy looks always positive (i performed several docking) and also the internal energy difference complex - free molecules looks positive, so in principle the two molecules should not like each other. On the other hand, when I re-compute the binding affinity with prodigy, I get negative values, meaning that the docked conformation i preferred.  
For example, the pdb of the best docked conformation have data like these (which units?)  
REMARK Desolvation energy: -14.3262  
REMARK Internal energy free molecules: -19248.3  
REMARK Internal energy complex: -18658.4  
REMARK Binding energy: 182.598

while the haddock output is like  
HADDOCK score -133.7 +/- 0.6  
Cluster size 132  
RMSD from the overall lowest-energy structure 2.2 +/- 2.4  
Van der Waals energy -77.8 +/- 5.9  
Electrostatic energy -297.0 +/- 45.5  
Desolvation energy -13.6 +/- 2.6  
Restraints violation energy 170.6 +/- 14.7  
Buried Surface Area 2013.0 +/- 35.4  
Z-Score -2.3

and the prodigy output is like  
cluster2\_1 -11.2 6.5E-09

They look contradictory to me , but I’m sure there is something I’m getting wrong from these numbers.  
Thanks for any help

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<div class="post-metadata">

**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\
**Post date:** [October 15, 2021, 10:09am UTC](https://ask.bioexcel.eu/t/binding-energy-of-docked-complex/3299/2 "2021-10-15T10:09:25Z")

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The HADDOCK score is the relevant value to look at.

In this case the score is -133.7

But do remember that docking scores are not equal to binding affinities… Little to zero correlation here!

See for example:

P.L. Kastritis and A.M.J.J. Bonvin [On the binding affinity of macromolecular interactions: daring to ask why proteins interact](https://doi.org/doi:10.1098/rsif.2012.0835) _J. R. Soc. Interface_, _10_, doi: 10.1098/rsif.2012.0835 (2013).

P. Kastritis and A.M.J.J. Bonvin [Are scoring functions in protein-protein docking ready to predict interactomes? Clues from a novel binding affinity benchmark.](https://doi.org/doi:10.1021/pr9009854) _J. Proteome Research_, _9_, 2216-2225 (2010).