Nuclc. Acids. Res. OUP
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JenPep

http://www,jenner.ac.uk/Jenpep2

McSparron, H, Blythe, MJ, Zygouri, C, Doytchinova, IA, Flower, DR

Edward Jenner Institute for Vaccine Research, Compton, Newbury, Berkshire, RG20 7NN

Contact   darren.flower@jenner.ac.uk


Database Description

From the perspective of human disease, a proper understanding of the immune system is vital. Indeed, the immune system has not only evolved to combat the threat from infectious disease, but immunological mechanisms play an equally pivotal role in other areas of human disease, such as autoimmunity, allergy, and cancer. One of the principal goals of Immunoinformatics, the application of molecular informatic techniques to the immune system, is to develop computational vaccinology and apply it to the search for new vaccines. At the heart of computational vaccinology are the twin problems of characterizing and predicting epitopes. To aid in this endeavour we have developed JenPep, an integrated relational database system for functional and quantitative data on peptide binding to biomacromolecules within immunobiology. It is the first in its class to concentrate on thermodynamic measurements, thus complementing existing system. JenPep contains five types of data: (i) quantitative measures for peptide binding to class I and class II MHC (12336 entries); (ii) a compendium of T-cell epitopes (3218 entries); (iii) quantitative measures for peptide binding to the TAP peptide transporter (441 entries); (iv) affinity measures for the formation of the peptide-MHC-TCR complex (49 entries); and (v) a compilation of B-cell epitopes (816 entries). The current version is a bespoke system using open source postgreSQL as the database engine and a graphical user interface (GUI) written in perl/HTML. The database is freely available from the URL: http://www.jenner.ac.uk/JenPep. Development of JenPep continues.

Recent Developments

Since the initial development of JenPep [1], we have increased both the size and scope of the database as well as implementing it within a postgreSQL database with a specially written perl/HTML interface. The number of data for our initial 3 categories (TAP and MHC binding and T-cell epitopes) has increased, and we have also introduced and populated two new categories: B-cell epitopes and peptide-MHC-TCR complex formation.

REFERENCES

Blythe, MJ, Doytchinova, IA, Flower, DR (2002). JenPep, a database of quantitative functional peptide data for immunology. Bioinformatics 18 434-439.

Category   Intermolecular Interactions

 

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