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Submitting a query to the Food Allergen Database (FAD)

You can use the following types of input to browse the Food Allergen Database:

• the UniProt ID, such as P00711;
• or the allergen name, such as Bos d 5.0101.
• or the first three letters of the genus (for example, Bos) .

If you are unsure of the UniProt ID or the name of the allergen you are interested in, you can access the entire database by typing Full in the query field.

Results of the queries

The information for each allergen is divided into three sections: the General, the Structural, and the Epitope information.

   General Information

The allergen info section includes:

• Allergen parent: the name of the allergen from which the isoform originates.
• Common name: the common name of the organism in which the allergen is expressed.
• Scientific name: the scientific name of the organism in which the allergen is expressed.
• The WHO/IUIS Allergen Nomenclature: information indicating whether the allergen is approved by the World Health Organization and the International Union of Immunological Societies allergen nomenclature or not.
• Allergenic tissue(s): tissue(s) in which the allergen is expressed (e.g., muscle, seed, milk).
• Enzyme classification: EC code; the field is empty if the allergen is not an enzyme.
• Taxonomy ID: taxonomic ID of the organism in which the allergen is expressed.

The sequence info section includes:

• UniProt sequence: the UniProt ID of the allergen along with the link to the sequence in FASTA format.
• Allergome access: the ID of the allergen in the Allergome database along with the link to Allergome.
• NCBI ID: the NCBI ID for food allergens without a UniProt ID; this field is empty if the allergen has a UniProt ID.
• Protein name: the name of the protein, provided by UniProt; this field is empty if the allergen has no UniProt ID.
• UniProt annotation: indicates whether the allergen has a status of Reviewed or Unreviewed in UniProt; this field is empty if the allergen has no UniProt ID.
• Sequence length: number of amino acids in the sequence.

The Gene Ontology, InterPro and SupFam sections include:

• Gene Ontology: the Gene Ontology codes associated with the allergen.
• InterPro: InterPro families of the allergen.
• SupFam: Superfamily annotation of the allergen.

   Structural Information

In this section you will find a table showing all the allergen structures available in FAD. The following data are provided:

• PDB: the PDB code of the structure. If the structure is an AlphaFold model, the UniProt ID is provided.
• Method: the method used to determine or predict the structure. Possible values include X-ray, NMR, CryoEM, Neutron diffraction, and AlphaFold (either retrieved from the AlphaFold database or modeled in-house for allergens lacking an available AlphaFold model).
• Resolution: the resolution (in Å) of structures resolved by X-ray crystallography. Not applicable for NMR or AlphaFold models.
• Chain: the chain(s) corresponding to the allergen sequence in the PDB entry.
• Sequence position: the sequence region covered by the structure.
• R-value: the R-value of structures resolved by X-ray crystallography, reflecting the agreement between the model and the diffraction data.

A representative structure is displayed at the top of the page. It is selected from all available structures for the allergen according to the following priority criteria:

1. Experimentally resolved structures are given top priority, with the following sub-priorities: (1) X-ray crystallography, (2) NMR, (3) CryoEM, (4) Neutron diffraction. If no experimental structure is available, an AlphaFold model is used as the representative.
2. Among structures obtained with the same method, priority is given to the one covering the largest sequence region.
3. Among structures with the same sequence length, priority is given to the one with the lowest resolution value (highest resolution quality), when available.
4. Among structures with the same resolution, priority is given to the one with the lowest R-value, when available.

For allergens represented by an AlphaFold model, two complementary quality metrics are provided to assess the reliability of the predicted structure:

• pLDDT (predicted Local Distance Difference Test): a per-residue confidence score ranging from 0 to 100. Each residue in the 3D structure is color-coded according to its confidence level:
  • Dark blue (>90): very high confidence
  • Light blue (70–90): confident
  • Yellow (50–70): low confidence
  • Orange/red (<50): very low confidence — region potentially disordered
  The average pLDDT across the full-length structure is also reported as a global quality indicator.
• PAE (Predicted Aligned Error): shown as a 2D heatmap, it represents the expected positional error (in Å) between pairs of residues when the structure is aligned. Low PAE values (darker cells) indicate high confidence in the relative orientation of the corresponding residues or domains. This metric is particularly informative for assessing multi-domain proteins, where it reflects the reliability of inter-domain orientations.

Together, pLDDT and PAE provide both local (per-residue) and global (inter-domain) assessments of structural reliability for AlphaFold models.

   Epitope Information

When epitopes are available for a given allergen, the Epitope page provides three complementary views: a 3D structure visualizer, a sequence-based mapping, and a detailed epitope table. All epitope data are sourced from the Immune Epitope Database (IEDB), with the search restricted to food allergy entries only.

▸ 3D Epitope Visualizer

The interactive 3D viewer displays the representative structure of the allergen (selected according to the criteria described in the Structural Information section), with epitope residues color-coded as follows:

• ● Red: Linear epitope(s) — continuous stretches of amino acids experimentally identified as epitopes.
• ● Magenta: Discontinuous (conformational) epitope(s) — spatially adjacent residues that form an epitope only in the folded 3D structure.
• ● Blue: Non-epitope residues — regions of the protein not associated with any known epitope.

The viewer is fully interactive: the structure can be rotated, zoomed, and explored in three dimensions. When multiple epitopes are available, pagination buttons (e.g., 1, 2…) allow navigation between individual epitopes, each highlighted separately on the structure.

▸ Sequence-Based Epitope Mapping

Below the 3D viewer, the full amino acid sequence of the representative structure is displayed with epitope regions color-highlighted directly on the sequence. The sequence is numbered every 50 residues to facilitate positional reference. This view provides a linear complement to the 3D visualization, making it easier to identify the exact positions and overlaps of epitope regions within the protein sequence.

▸ Epitope Table

A detailed table lists all epitopes annotated for the allergen. Each row corresponds to one epitope entry from the IEDB. The following columns are provided:

• IEDB ID: the unique identifier of the epitope in the Immune Epitope Database (IEDB). Clicking the ID redirects to the full IEDB epitope record.
• Epitope type: the structural nature of the epitope — Linear (defined by a continuous amino acid sequence) or Discontinuous (conformational, defined by spatially adjacent residues in the folded structure).
• Assay : the immunological nature of the epitope — B-cell or T-cell. B-cell epitopes include IgE-binding epitopes, which are the primary mediators of IgE-mediated allergic responses. This annotation allows users to filter epitopes by immunological relevance and focus specifically on IgE-relevant targets when investigating allergenic mechanisms.
• Start / End position: the positions of the first and last amino acid of the epitope in the full allergen sequence. These values are set to 0 for discontinuous epitopes, as their residues are not contiguous.
• Epitope amino acids: the amino acid sequence of the epitope. For discontinuous epitopes, each contributing residue is listed individually in the format 'amino acid type — sequence number' (e.g., K30, D55, E102).
• Start / End mapping: the positions of the epitope mapped onto the sequence of the representative structure (which may differ from the full allergen sequence if the structure covers only a partial region). These values enable direct correspondence between the table and both the 3D viewer and the sequence mapping display above.

Downloading the results

Users can download the allergen database in several ways. All download options are accessible by typing Full in the query field to access the entire database. From there, the table can be exported in CSV format. A filter menu allows the user to restrict the table before downloading. Finally, the fields to be included in the download can be customized via the Advanced download menu.