HADDOCK2.4 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 HADDOCK2.4 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.