Scoring workflow

Defining a haddock3 configuration file

This example illustrates the use of Haddock3 for scoring purposes. In contrast to HADDOCK2.X, Haddock3 can score a heterogenous set of complexes within one run/workflow. In this example, four different types of complexes are scored within the same workflow:

  • an ensemble of 5 models taken from CAPRI Target161
  • a protein-DNA complex (model taken from our protein-DNA docking example)
  • two models of a protein-protein complex (taken from our protein-protein docking example)
  • a homotrimer model (taken from our protein-homotrimer docking examples)

Three scoring workflows are illustrated:

  • emscoring-test.cfg: Only a short energy minimisation is performed on each model using [emref] module.
  • mdscoring-test.cfg: A short molecular dynamics simulation in explicit solvent (water) is performed on each model using [mdref] module. In that case contact AIRs (contactairs = true), dihedral angle restraints on secondary structure element (ssdihed = alphabeta) and DNA restraints (dnarest_on = true) are automatically defined.
  • capri-scoring-test.cfg: An example scoring pipeline using in the CAPRI55 competition, where energy minimisation module ([emref]) is followed by FCC clustering ([clustfcc]) and selection of the top 2 models per cluster ([seletopclusts] with top_models = 2). Then a short molecular dynamics simulation in explicit solvent (water) is performed on each model using [mdref] module and the models are clustered again.

The model listings with their associated HADDOCK scores can be found in a .tsv file in the stage 01_xxx directory of the respective runs.

Using scoring command line

Haddock3 also contain a simple command line interface that allows you to score a single pdb file. To do so, just run:

haddock3-score complex.pdb

This command is a short-cut to the following parameter file, and therefore can be really handy, as it simplify a lot the procedure, but is limitted to the scoring of a single model.

run_dir = "tmp_score"
molecules = "complex.pdb"
[topoaa]
[emscoring]

For more details on the haddock3-score CLI, please refere to this section.