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HADDOCK2.4 user manual



DEFAULT RUN SETTINGS


Associated HADDOCK params: Modifiable by EASY users Modifiable by GURU users

Other: External link

Input structures
  • File format for the PDB files must follow the wwPDB standards wwPDB format standards
  • 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 and the different models should be surrounded by MODEL and ENDMDL records).
  • It is possible to either download a PDB directly from the RCSB database or to provide your own PDB. pdb_mode
  • 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 - it0: 1000 (with Ntrial=5 and sampling of 180 degrees-rotated solutions)
    ntrials structures_0 rotate180_0
  • Semi-flexible refinement - it1: 200 structures_1
  • Water refinement - itw: 200 waterrefine

Ambiguous Interaction Restraints (AIRs)

  • Only active/passive residues can be used as restraints in EASY mode, no restraints file or center-of-mass restraints can be provided.
    activereslist passivereslist
  • You can choose to either defined passive residues yourself, to no provide any or to let HADDOCK defined them as the closest residues from the active residues you have provided. In automatic mode, the passive residues are taken as all residues that have a solvent accessibility higher than 15% and at least one atom at less than 6.5A from any atom of an active residue.
    auto_passive auto_passive_radius
  • By default, 50% of the AIRs will be randomly deleted for each docking trial. noecv

Flexibility treatment

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

Protonation state of histidines

  • The protonation state of histidines is automatically defined by using MolProbity/Reduce.
    his_#_state MolProbity

Co-factors and ligands

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

DNA/RNA restraints (if applicable)

  • The type of the molecule must have been explicitly set by the user. moleculetype
  • Backbone dihedral angles restraints: values measured from input structure.
    Pucker restraints: measured from input structure.
    Planarity restraints: on a per base basis.
    Hydrogen bond restraints (DNA only): from detected base-pairs.

Clustering parameters

  • Default method: FCC (vs RMSD) clust_meth
  • Default cut-off: 0.6 clust_cutoff
  • Default minimum size: 4 clust_size

Final scoring

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

    HADDOCK-score it0 = 0.01*Evdw + 1.0*Eelec + 1.0*Edesolv + 0.01*Eair - 0.01*BSA


    HADDOCK-score it1 = 1.0*Evdw + 1.0*Eelec + 1.0*Edesolv + 0.1*Eair - 0.01*BSA


    HADDOCK-score itw = 1.0*Evdw + 0.2*Eelec + 1.0*Edesolv + 0.1*Eair

    w_elec w_vdw w_desolv

Restraints validation

  • All restraints (distances, hbonds, dihedral angle, RDCs and diffusion anisotropy) are submitted to a strict validation by the server. They should comply to CNS syntax.
    dihedralfile unambigtblfile tblfile pcsfile rdcfile tensorfile hbondfile CNS syntax danfile