Alexandre Bonvin bio photo

Computational Structural Biology group focusing on dissecting, understanding and predicting biomolecular interactions at the molecular level.

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HADDOCK2.2 scoring function

The HADDOCK scoring function consists of a linear combination of various energies and buried surface area. It differs for the various docking stages (rigid body (it0), semi-flexible refinement (it1) and explicit solvent refinement(water)).

The scoring is performed according to the weighted sum (HADDOCK score) of the following terms:

  • Evdw: van der Waals intermolecular energy
  • Eelec: electrostatic intermolecular energy
  • Eair: distance restraints energy (only unambiguous and AIR (ambig) restraints)
  • Erg: radius of gyration restraint energy
  • Esani: direct RDC restraint energy
  • Evean: intervector projection angle restraints energy
  • Epcs: pseudo contact shift restraint energy
  • Edani: diffusion anisotropy energy
  • Ecdih: dihedral angle restraints energy
  • Esym: symmetry restraints energy (NCS and C2/C3/C5 terms)
  • BSA: buried surface area
  • dEint: binding energy (Etotal complex - Sum[Etotal components] )
  • Edesol: desolvation energy

The default scoring function settings of HADDOCK are for protein-protein complexes and use the following weights:

* HADDOCKscore-it0   = 0.01 Evdw + 1.0 Eelec + 1.0 Edesol + 0.01 Eair - 0.01 BSA
* HADDOCKscore-it1   =  1.0 Evdw + 1.0 Eelec + 1.0 Edesol +  0.1 Eair - 0.01 BSA
* HADDOCKscore-water =  1.0 Evdw + 0.2 Eelec + 1.0 Edesol +  0.1 Eair

Note: Additional terms are used if other types of experimental restraints are used. Refer to values defined in run.cns (and accessible at the guru level of the HADDOCK portal) for their default settings.

Note: For protein-ligand (small molecule) docking we recommend to change the weight of Evdw(it0) to 1.0 and Eelec(water) to 0.1.

Note: For protein-nucleic acids docking we recommend to set the Edesol weight to 0 for all stages

The structure with the smallest weighted sum will be ranked first.