Alanine Scanning module
Submodules
Module contents
HADDOCK3 module for alanine scan.
This module is responsible for the alanine (or any other residue) scan analysi of the models generated in the previous step of the workflow. For each model, the module will mutate the interface residues and calculate the energy differences between the wild type and the mutant, thus providing a measure of the impact of such mutation. Such difference (delta_score) is always calculated as:
delta_score = score_wildtype - score_mutant
Therefore, a positive delta_score indicates that the mutation is destabilizing while a negative delta_score indicates that the mutation is stabilizing.
If cluster information is available, the module will also calculate the average energy difference for each cluster of models. For each amino acid, a Z score is calculated as:
Z = (delta_score - mean) / std
where mean and std are the mean and standard deviation of the delta_score over all the amino acids.
The module will also generate plots of the alanine scan data, showing the distribution of the delta_score (and every component) for each amino acid at the interface.
You can use the parameters below to customize the behavior of the module:
chains: list of chains to be considered for the alanine scan. In some cases you may want to limit the analysis to a single chain.
output_mutants: if True, the module will output the models with the mutations applied (only possible if there is only one model)
output_bfactor: if True, the module will output the non-mutated models with the rescaled delta_score in the B-factor column
plot: if True, the module will generate plots of the alanine scan data
scan_residue: the residue to scan (default is ‘ALA’)
resdic: list of residues to be used for the scanning. An example is:
>>> resdic_A = [1,2,3,4] >>> resdic_B = [2,3,4]
- class haddock.modules.analysis.alascan.HaddockModule(order, path, *ignore, init_params=PosixPath('/opt/hostedtoolcache/Python/3.10.16/x64/lib/python3.10/site-packages/haddock/modules/analysis/alascan/defaults.yaml'), **everything)[source]
Bases:
BaseHaddockModule
HADDOCK3 module for alanine scan.