Alexandre Bonvin bio photo

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

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Settings for running with bioinformatic predictions

The previous version of the HADDOCK server (2.2) had a dedicated interface with custom settings for use with bioinformatics predictions. In order to replicate those settings in the HADDOCK2.4 submission interface changes manually the following parameters (needs Expert access level):

In the “Distance Restraints” section:

  • Number of partitions for random exclusion1.14285714286

In the “Sampling parameters” section:

  • Number of structures for rigid body docking10000
  • Number of trials for rigid body minimisation1
  • Number of structures for semi-flexible refinement400
  • Number of structures for the final refinement400
  • Number of structures to analyze -> 400