RNA Scanning module
Submodules
Module contents
HADDOCK3 module for RNA base scan.
This module performs a mutagenesis scan of RNA bases for the model(s) generated in the previous step of the workflow. For each model, every selected interface nucleic acid residue is mutated into each of the four RNA bases (A, C, G and U) and the differences in the haddock score and its individual components between the wild type and each mutant are calculated, thus providing a measure of the impact of such mutations. By default, all four possible bases are tested for every selected interface nucleotide (the wild-type base is skipped). Such difference (delta_score) is always calculated as:
delta_score = score_wildtype - score_mutant
As the score are typically negative with lower values being better, a _positive_ delta_score indicates that the mutation is stabilizing while a _negative_ delta_score indicates that the mutation is destabilizing.
If cluster information is available, the module will also calculate the average haddock score difference for each cluster of models. For each mutation, 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 mutations.
The module will also generate plots of the RNA scan data, showing the distribution of the delta_score (and every component) for each mutation at the interface.
You can use the parameters below to customize the behavior of the module:
scan_bases: list of target bases to be tested for each nucleotide. By default all four RNA bases (A, C, G, U) are tested.
chains: list of chains to be considered for the RNA 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 RNA scan data
splitplot: if True, the scan plot shows one panel per energy component; if False (default) all components are overlaid in a single panel
resdic: list of residues to be used for the scanning. An example is:
>>> resdic_A = [1,2,3,4] >>> resdic_B = [2,3,4]
Only nucleic acid (RNA) residues at the interface are mutated; protein and other residues are ignored.
When applying a mutation, the ribose-phosphate backbone is always kept. For mutations between bases of the same ring type (purine <-> purine, i.e. A <-> G, or pyrimidine <-> pyrimidine, i.e. C <-> U), the shared base ring atoms are also kept so that the base orientation is preserved and CNS only rebuilds the differing substituents. For cross-type mutations (purine <-> pyrimidine), the three glycosidic-region anchor atoms are kept and renamed to their counterpart in the target ring system (pyrimidine N1/C2/C6 <-> purine N9/C4/C8), so that the base orientation is preserved and CNS rebuilds the rest of the new base.
- class haddock.modules.analysis.rnascan.HaddockModule(order, path, *ignore, init_params=PosixPath('/opt/hostedtoolcache/Python/3.10.20/x64/lib/python3.10/site-packages/haddock/modules/analysis/rnascan/defaults.yaml'), **everything)[source]
Bases:
BaseHaddockModuleHADDOCK3 module for RNA base scan.