Scoring modules
[emscoring] module
EM scoring module.
This module performs energy minimization and scoring of the models generated in the previous step of the workflow. No restraints are applied during this step.
The default HADDOCK scoring function in the [emscoring] module is therefore the following:
For a detailed explanation of the components of the scoring function, please have a look here.
Notable parameters
The most important parameters for the [emscoring] module are:
nemsteps: number of energy minimization stepsper_interface_scoring: output per interface scores in the PDB header (default: False)
More information about [emscoring] parameters can be accessed here or retrieved by running:
haddock3-cfg -m emscoring
[mdscoring] module
MD scoring module.
This module will perform a short MD simulation on the input models and score them. No restraints are applied during this step.
The same scoring function as in the [emscoring] module is used:
Notable parameters
The most important parameters for the [mdscoring] module are:
nemsteps: number of energy minimization stepsper_interface_scoring: output per interface scores in the PDB header (default: False)waterheatsteps: number of MD steps for heating up the systemwatersteps: number of MD steps at 300Kwatercoolsteps: number of MD steps for cooling down the system
More information about [mdscoring] parameters can be accessed here or retrieved by running:
haddock3-cfg -m mdscoring
prodigy modules
Two modules are using the Prodigy methods for the evaluation of binding affinity. As this scoring is specific to either proteins or ligands, two modules are available, and should be used depending on the system you are working on:
- [
[prodigyprotein]]: for the prediction of protein-protein binding affinities - [
[prodigyligand]]: for the prediction of protein-ligand binding affinities