|Department of Biochemistry and Molecular Biology||Sealy Center for Structural Biology||Computational Biology|
SDAP - Structural Database of Allergenic Proteins
SDAP (Structural Database of Allergenic Proteins) is a Web server that provides database information and various cobputational tools for the study of allergenic proteins. The database component of SDAP contains information the allergen name, source, sequence, structure, IgE epitopes, and literature references, and links to the major protein (PDB, SWISS-PROT, PIR, NCBI) and literature (PubMed, MEDLINE) servers. The computational component in SDAP uses an original algorithm based on conserved properties of amino acid side chains to identify regions of known allergens similar to user-supplied peptides or selected from the SDAP database of IgE epitopes. This and other bioinformatics tools can be used to rapidly determine potential cross-reactivities between allergens and to screen novel proteins for the presence of IgE epitopes they may share with known allergens.
SDAP was developed guided by the allergens list from the IUIS (International Union of Immunological Societies) website, http://www.allergen.org, supplemented with information from literature and from major sequence (SwissProt, PIR, and NCBI) and structure (PDB) databases. As there is no public database summarizing information on known epitopes of allergenic proteins, the IgE epitope list in SDAP is based solely on primary literature sources. SDAP is the first allergen database that allows a user to retrieve IgE epitopes and identify similar regions in other allergenic proteins.
The following SDAP options are available from the left column of each page:
In its present version, SDAP allows searches restricted to the following fields: allergen name (according to the IUIS website listing), scientific and common name for the species, general source of the allergens, and allergen description. The information from each search field was initially compiled from the IUIS website, http://www.allergen.org, and supplemented with information from literature. For acceptable search terms the user should consult the IUIS website.
All queries implement a case insensitive search for the presence of the
query term in a record from the database. For example, a search for fl in
the field "allergen - scientific name" will give the result Asp fl 13.
Allergens are designated according to the scientific name of their source: the first three letters of the genus, one space, the first letter of the species, one space, and an Arabic number. When confusion can arrise, an additional letter is added after the first three letters of the genus or after the first letter of the species: Mala f 1, Asp fl 13, Pru ar 1.
To find an allergen in SDAP, use only IUIS accepted allergen names. The spaces are mandatory, and the final number must be Arabic, and not Roman. Some allergen names from the literature do not follow the IUIS recommendations, have missing spaces, or use Roman numbers instead Arabic (i.e., I instead 1). The use of such names as search terms in SDAP will not provide any search result.
A list with all allergens from a ceratin source can be obtained by selecting the search field source - scientific name and then entering in the Search Term field the desired scientific name of the allergen source.
For example, a search for Juniperus gives as result a list of allergens from Juniperus ashei, Juniperus oxycedrus, Juniperus sabinoides, and Juniperus virginiana.
When the common name of the source is known, a list with all allergens from a ceratin source can be obtained by selecting the search field source - common name and then entering in the Search Term field the desired common name of the allergen source.
Below is a list of acceptable search terms for the search field
For example, a search for pollen in the field allergen type will give as result a list of all allergens from weed, grass, and tree pollen.
Some acceptable search terms for the search field allergen description:
SDAP can be used to identify allergen regions having an identical sequence with a peptide provided by the user. The search is made in the database ALL_SEQ containing more than 1800 sequences. The database ALL_SEQ contains allergen sequences from literature and retrieved from NCBI using the keyword "allergen". Some sequences are fragments, or represent sequences from patents. The Peptide Match function takes the peptide sequence supplied by the user and provides a list of all sequences with regions that match the peptide.
The SDAP sequence similarity ranking takes as input a peptide provided by the user
and gives as output a list of proteins from the ALL_SEQ database that have
regions highly similar with the query peptide, in the decresing order of
This original procedure implements a protein sequence
similarity search based on the five dimensional descriptors
E1-E5 of amino acids properties derived
from a pool of 237 physico-chemical properties [Venkatarajan, 2001].
The similarity between two sequences A and B, each one consisting
of N residues, is computed with the property distance function PD:
When available, the search results for a specific allergen include also a table with epitopes. Each epitope from such a table can be submitted to the Peptide Match or Peptide Similarity computational tools. The epitope database from SDAP is based solely on primary literature sources, and is constantly updated.