Alexandre Bonvin bio photo

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

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Advanced refinement of molecular complexes

HADDOCK2.2 provides a dedicated web interface to run a refinement on a molecular complex. This nice feature is accessible via the refinement interface of HADDOCK2.2 and required a registered account with Expert level access.

As input, only a PDB file for each partner of the complex (for a unique PDB file, you need to specify two different chain IDs). You can optionally change the weight of the different energy terms used in the HADDOCK score to assess the quality of your models. A fine-tuned set of parameters will be then used by HADDOCK to perform the water refinement.

However, it is sometimes interesting to tune this default set of parameters to cope with particular cases like unusual histidine protonation states, multibody docking, ensemble and/or cross-docking, etc. To do so, it is possible to use the HADDOCK Guru interface (needs Guru access level) and change few parameters to only use the refinement capability of HADDOCK:

In the “Distance Restraints” section:

  • Define center of mass restraints to enforce contact between the molecules → True
  • Define surface contact restraints to enforce contact between the molecules → True

In then “Sampling parameters” section:

  • Number of structures for rigid body docking (it0) → Same as the number of models you want HADDOCK to generate in water
  • Number of structures for rigid body docking (it1) → Same as the number of models you want HADDOCK to generate in water
  • Sample 180 degrees rotated solutions during rigid body EM → False

In then “Advanced Sampling Parameters” section:

  • Perform cross-docking → False
  • Multiply the number of calculated structures by all combinations → True
  • Randomize starting orientations → False
  • Perform initial rigid body minimisation → False
  • Allow translation in rigid body minimisation → False
  • Number of MD steps …*4 → 0 for the 4 values (respectively 500/500/1000/1000 by default)

Those few changes will force HADDOCK to only perform a water refinement as if you would have submitted your run via the refinement interface. You can then change any other parameters to suit your needs and submit your run in the guru interface.