Easy interface settings

The following default settings are used for runs submitted to the easy interface.

Input structures:

• The server supports docking from ensembles of structures. For this simply submit a PDB file containing multiple models (Note that they should all contain exactly the same number of atoms).
• If within one submitted structures multiple unconnected bodies are detected, additional distance restraints will automatically be defined to keep the bodies together (e.g in an antibody).

Number of structures generated:

• rigid-body EM: 1000 (with Ntrial=5 and sampling of 180o-rotated solutions)
• semi-flexible refinement: 200
• water refinement: 200

Ambiguous interaction restraints (AIRs) treatment:

• By default, 50% of the AIRs will be randomly deleted for each docking trial

Restraints validation:

• All restraints (distances, hbonds, dihedral angle, RDCs and diffusion anisotropy are are submitted to a strict validation by the server. They should comply to CNS syntax.

Flexibility treatment:

• Semi-flexible residues are automatically defined from an analysis of intermolecular contacts (<5.0A)

Protonation state of histidines:

• The protonation state of histidine is automatically defined by querying the Whatif web server

Co-factors and ligands:

• Missing parameter and topology files for co-factors and small ligands are automatically obtained from the PRODRG web server

The following DNA/RNA restraints are used if one of the molecule is defined as such:

• Backbone dihedral angles restraints: values measured from input structure
• Pucker restraints: measured from input structure
• Planarity restraints on a per base basis
• For DNA: hydrogen bond restraints from detected base-pairs

Clustering parameters:

• FCC cut-off = 0.75
• minimum number of members in a cluster: 4

Final scoring:

The reported scores and energies are averages calculated over the top four members of a cluster. The HADDOCK score is defined as:

• HADDOCK-score = 1.0*EVDW+0.2*EELEC+1.0*EDesolvation

For more information on the various parameters visit the HADDOCK online manual

Expert, Guru and Multibody interfaces

Those three interfaces give increased control on various HADDOCK parameter settings. The defaults are the same as for the easy interface

Prediction interface

The prediction interface is based on optimized settings for the use of HADDOCK with bioinformatic interface predictions (S.J. de Vries and A.M.J.J. Bonvin, manuscript in preparation)

It should be used with bioinformatic interface predictors that over-predict the interface, such as CPORT

It uses the same settings as the easy interface, with the following modifications:

Ambiguous interaction restraints (AIRs) treatment:

87.5 % of the AIRs will be randomly deleted for each docking trial

Sampling parameters:

• Number of rigid body structures: 10 000
• Number of docking trials per rigid body structure (Ntrial): 1
• Number of flexible refinement structures: 400
• Number of water refinement structures: 400
• Number of analyzed structures: 400

Refinement interface

The refinement interface turns off the rigid body stage (it0) and the flexible refinement (it1), and performs only a water refinement.

It uses the same settings as the easy interface, with the following modifications:

Ambiguous interaction restraints (AIRs) treatment:

• All experimental restraints are disabled. Center-of-mass restraints and surface contact restraints are enforced

Sampling parameters:

• The rigid body stage and it1 are disabled; only an initial energy minimization is performed
• Every uploaded structure is refined 20 times in water
• Cross-docking is disabled: if you upload two ensembles, protein 1 of ensemble A is “docked” only with protein 1 of ensemble B, not with protein 2, 3, etc