HADDOCK2.4 user manual
DEFAULT RUN SETTINGS
Associated HADDOCK params: Modifiable by EASY users Modifiable by GURU users
Other: External link
- 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.
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.
- By default, 50% of the AIRs will be randomly deleted for each docking trial. noecv
Semi-flexible residues are automatically defined from an analysis of intermolecular contacts (<5.0A).
Protonation state of histidines
The protonation state of histidines is automatically defined by using MolProbity/Reduce.
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.
- Default method: FCC (vs RMSD) clust_meth
- Default cut-off: 0.6 clust_cutoff
- Default minimum size: 4 clust_size
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*Eairw_elec w_vdw w_desolv
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