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 HADDOCK2.4 submission interface this is presented as an option in Step 2 (needs Expert access level). When selecting this option the following changes will automatically be applied:

In the “Distance Restraints” section:

  • Number of partitions for random exclusion → 1.1428

In the “Sampling parameters” section:

  • Number of structures for rigid body docking → 10000
  • Number of trials for rigid body minimisation → 1
  • Number of structures for semi-flexible refinement → 400
  • Number of structures for the final refinement → 400
  • Number of structures to analyze -> 400