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BactMentha data come from multiple databases. First protein-protein interaction data are taken from IMEx Consortium databases for each host taxon. Complementary informations for interacting proteins are taken from Uniprot. Moreover, NCBI blastp has been used against Virulence Factor Database (VFDB) and BastionHub sequences to annotate the bacterial proteins. Information related to detection method, the interaction type and the PubMed ID are also retrieved. Finally, binding interfaces are inferred via the mimicINT workflow and interacting pair complex structure, when available, have been predicted using AlphaFold3 via MassiveFold.

PA or 'Protein Annotation' is related to the bacterial annotations available in the BactMentha Database. Those information come from Virulence Factor Database (VFDB) and BastionHub. CC or 'Cellular Component' refers to localization annotations of either the bacterial or the human protein, or both. The available annotations of subcellular localization are taken from Uniprot. The annotation can be 'exact' if it corresponds directly to the protein or 'canonical fallback' when the annotation is transferred to isoforms. BR or 'Binding Regions' refers to the known binding regions between two interactors (detected experimentally). This information is taken directly from the IMEx Consortium databases. MI or 'mimicINT Interfaces' refers to the predicted binding interfaces between two interactors. These annotations are generated by the mimicINT workflow. Finally, AF or 'AlphaFold complexes' refers to only bacteria-human interactions, with bacterial proteins having PA annotations, for which complex structures have been predicted using AlphaFold3 via MassiveFold.

Yes, you can download them via the buttons located at the upper right corner of the browse page. The 'Show/Hide columns' button allows you to mask or display columns on the current result table. The 'CSV + annotations to CSV' button allows you to download the current table (e.g., after filtering in the headers and selecting columns of your interest) and the annotation tables (bacterial protein annotations, cellular components, binding regions, mimicINT interfaces and AF3 predictions) for the corresponding interactions in the filtered table. The 'CSV' button allows you to download only the current filtered table (without the additionnal annotation tables). Finally, the 'Excel' button permits also to download the current table only in an Excel format file.

The unit corresponds to amino acid positions. For example, for this Binding Region table:

Identifier A	Feature A	Feature start A	Feature end A	Identifier B	Feature B	Feature start B	Feature end B
Q8X482	binding-associated region	221	314	O08816	binding-associated region	193	501

There is binding region information for the interaction between the bacterial protein (A columns) Q8X482 and the host protein (B columns) O08816. The experimentally detected binding region in protein Q8X482 spans from the amino acid position 221 to the amino acid position 314, and in the protein O08816 it spans from the position 193 to the position 501.
This applies to mimicINT Interface tables as well.

BactMentha adheres to the HUPO Proteomics Standards Initiative on Molecular Interactions guidelines. You can find the Molecular Interaction ontology term definitions here.

The MI score provided by BactMentha is retrieved directly from IMEx Consortium data. Its value is calculated taking into account three factors : the detection method, the interaction type, and the number of publications that describe the given interaction. For more details, see the Intact Interaction Scoring documentation. This score can be used to select “high-confidence” interactions. In a paper published in Database in 2015 (PMID: 25652942) the authors state that "the optimal cutoff value for MI score is 0.485 (which is close to the heuristic cutoff of 0.45 proposed by IntAct)".

Yes, you can add a condition based on the WHO priority level or the Hazard group of the bacterial pathogen in the Advanced Search form.

WHO priority groups aims to guide/promote research of new antibiotics for multidrug resistant bacteria, which are, in turn, listed as "priority pathogens". On the other side, pathogens are classified into an hazard group depending on their pathogenicity to human, risk of infections, spread potential and availability of effective vaccine or treatment.