Threshold value

HADDOCK
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1

I have done the HADDOCK docking. I am getting the results for Cluster 1.

HADDOCK score

-100.5 +/- 2.7

Cluster size

62

RMSD from the overall lowest-energy structure

1.1 +/- 0.1

Van der Waals energy

-57.0 +/- 10.0

Electrostatic energy

-278.8 +/- 30.3

Desolvation energy

-4.8 +/- 5.8

Restraints violation energy

170.5 +/- 106.4

Buried Surface Area

1876.8 +/- 62.0

Z-Score

-1.1. .. I am getting this … I want to know if there is any threshold value for good docking results for the given parameter .. What do we consider this? . Help me out this. For general information about HADDOCK refer to HADDOCK – Bonvin Lab

2

Dear Priyanka,

Thanks for your interest in using HADDOCK for your research.

In general, there is not threshold values to consider a good docking result, as the HADDOCKscore depends on the size of the system and the amount of restraints.

To assess the quality of your run you can:

  • see if the best clusters have similar scores (+/- overlapping standard deviations), or is there a clear ‘winner’
  • if the models converged towards a given solution
  • do they satisfy the input restraints
  • can you identify classical interactions (hydrogen-bonds, pi-stacking, salt-bridges, etc…)
  • check if the obtained conformation resemble something known from the literature

With the hope this answer is helping you deciding

3

Thank you for your reply. one more question is that how can i get the interaction? with my receptor and peptide..

4

You can:

  • visually inspect your complex with your favorite molecular visualizing tool (e.g.: pymol, chimeraX, vmd)
  • this can also be performed online with Mol* for example
  • use tools that identify typical interactions (e.g.: BINANA, PLIP)