Immune Epitope Database

IEDB (Immune Epitope Database and Analysis Resource) www.immuneepitope.org Immune epitope database... 

At the epitope level, the Immune Epitope Database and Analysis Resource (IEDB) is the largest immune epitope database so far (http //www.immuneepitope.org/). IEDB has stored more than 65,000 antibody and T-cell epitopes since the database was established in 2004 (9). These immune epitopes cover various species (e.g., humans, nonhuman primates, and rodents) that have been well studied in the areas of infectious diseases (9). Because all stored epitopes in IEDB are manually curated from experimental studies, the data in IEDB have often been used as the gold standard for evaluating in silico epitope prediction tools (10). 

Peters B, Sidney J, Bourne P et al (2005) The immune epitope database and analysis resource from vision to blueprint. PLoS Biol 3 e91... 

Zhang Q, Wang P, Kim Y et al (2008) Immune epitope database analysis resource (IEDB-AR). Nucleic Acids Res 36 W513-W518... 

In the absence of reliable predictive methods for assessing potential immunological cross-reactivity, a comparative sequence analysis approach can be used to identify whether or not known epitopes from human proteins exist in a candidate vaccine antigen. The Immune Epitope Database (IEDB) provides a comprehensive reference data set for known epitopes.78 When screening potential vaccine candidates, the presence of known human-derived epitopes can be ruled out by comparison against the IEDB (www.iedb.org). 

Zhang Q, Wang P, Kim Y, Haste-Andersen P, Beaver J, Bourne PE, Bui HH, Buus S, Frankild S, Greenbaum J, Lund O, Lundegaard C, Nielsen M, Ponomarenko J, Sette A, Zhu Z, Peters B. Immune epitope database analysis resource (IEDB-AR). Nucleic Acids Res. 2008 36 W513-W518. Epub 2008 May 31. 

As a manufactured product, a vaccine is composed of several components. A vaccine antigen(s) is a required component for any vaccine. Such a vaccine antigen can be part of a whole organism (e.g., live attenuated vaccine), a protective protein antigen, or an immune epitope. A live attenuated vaccine usually does not require a vaccine adjuvant that functions as an immune stimulant. However, killed whole organism or subunit vaccines usually need vaccine adjuvants. Otherwise, a weak or nonexistent immune response will be induced. Other vaccine components include vaccine vectors and vaccine preservatives. Databases of these vaccine components are briefly introduced here. 

There are several types of vaccine antigens. The most common antigens used for vaccine development are protein antigens. Immune epitopes may also be manufactured and used for vaccine development. Other molecules can also be used as vaccine antigens (e.g., lipopolysaccharide) (6). The commonly used databases for protein and epitope antigens are introduced here. 

If a monoclonal antibody was generated by immunization with a full-length native protein rather than a peptide, then the immunized mouse will generate antibodies that recognize both linear and conformationally dependent epitopes. Only a small subset of these monoclonal antibodies will likely be useful for clinical use on formalin-fixed, paraffin-embedded tissue (FFPE) samples. Those that are useful tend to have epitopes that are linear the epitopes are not dependent on the protein s three-dimensional conformation (see Chapter 16). Therefore, for antibodies generated in response to immunization with full-length proteins, the peptides that serve as positive controls will be linear stretches of amino acids derived from the native protein sequence, as listed in protein databases. 

Nowadays, bioinformatics, especially in computational immunology expands itself and it is focused on analyzing large-scale experimental data and comparison (Tong and Ren 2009 Korber 2006). Immunology-related databases cover all other aspects of immune system processes and diseases and the web address, which are helpful for epitope designing and new dmg designing (Ross 1916). 

---