The antigenic regions of protein recognized by the binding sites of immunoglobulin molecules are called B-cell epitopes 1. These epitopes can be classified into two categories; i) conformational/discontinuous epitope, where residues are distantly separated in the sequence and brought into physical proximity by protein folding and, ii) linear/continuous epitope, comprised of a single continuous stretch of amino acids within a protein sequence that can react with anti-protein antibodies 23. Most of the B-cell epitopes were thought to be discontinuous. However, in late 1980s it was shown that this conformational restriction is not a necessary condition for the production of protein-reactive anti-peptide antibodies 4. The designing of the conformational epitopes is difficult and so experimental B-cell epitopes largely include linear epitopes. These linear epitopes can be exploited in the development of synthetic vaccines and disease diagnosis. A number of vaccines based on B-cell epitopes are currently under clinical phase trials against viruses 5, bacteria 6 and cancer 7. These epitopes are also important for allergy research and in determining cross-reactivity of IgE-type epitopes of allergens 8.

A large number of B-cell epitopes have been reported in the literature in last two decades. There is a need to collect and compile these epitopes to evaluate the performance of existing B-cell epitope prediction methods and to further develop better methods 910. We have observed that the performance of the existing physico-chemical scales is not very high 11. Recently, Blythe and Flower examined 484 amino acid propensity scales in predicting of B-cell epitopes and found that even the best set of scales and parameters performed only marginally better than random 12. The evaluation of the existing scales indicates that there is a need to develop better methods by using artificial intelligence techniques. The collection of B-cell epitopes should help in deriving new scales for accurate in silico prediction of linear epitopes. Also it will help the immunologist to understand the complex nature of immunogenic peptides and for the development of vaccines. There are many databases available on T-cell epitopes 131415. In contrast, there are limited number of databases on B-cell epitope for example JenPep 1617 and HIVDB 18. Recently, JenPep has been superseded by AntiJen 2.0, which has included peptides bound to MHC ligand, TCR-MHC Complexes, T cell epitope, TAP, B cell epitope molecules and immunological protein-protein interactions. AntiJen also contains peptide library, copy numbers and diffusion coefficient data. Though AntiJen provides information about different types of peptides (>24000 entries) from a single source but it provides limited information about B-cell epitopes and tools to analyze and retrieve the data. Recently, we have created a comprehensive database, Bcipep, of B-cell epitopes. Latest version of Bcipep contains 3031 entries, where each entry provides detailed description of a B-cell epitope. Currently, we have covered only the continuous B-cell epitopes. The aim of this database is to assist the scientific community working in the areas of synthetic peptide vaccines (based on B-cell epitopes) and allergy research. The database will complement the existing databases such as AntiJen 1617.

The PostgreSQL relational database management system (RDBMS) has been used for storing, retrieval and managing the data. The scripts, which provide interface between user and database, were written in PERL, CGIPerl and Pgperl. B-cell epitopes were collected from the literature (PubMed, http://www.ncbi.nlm.nih.gov/pubmed/; ScienceDirect, http://www.sciencedirect.com/). A large number of HIV epitopes were extracted from a book 18.

The aim of Bcipep database is to provide; i) comprehensive information about B-cell epitopes, ii) tools for extraction and analysis of this information and, iii) hyperlinks to related databases. The overall architecture of Bcipep database is shown in Figure 1.

Bcipep has following major web-based tools for retrieval and analysis of information in Bcipep database (Figure 1). These web tools have been designed to facilitate the user in retrieving information from database.

The database has the facility to submit data to Bcipep on-line via Internet. Users can submit information about their experimentally determined B-cell epitopes. We hope that immunologists will submit their information on B-cell epitope in Bcipep, similar to the sequence data at GenBank and SWISS-PROT. The Bcipep team will add more data from literature to maintain B-cell data up-to-date and cross check the data submitted by users to maintain quality of the data.

One of the major challenges in the field of subunit vaccine design is to identify the antigenic regions (B and T cell epitopes) that can generate antigen specific memory cells. Thus, the identification of regions/stretches on an antigen from the data pool of known epitopes is an important step in vaccine design. The Bcipep database would be very useful as it consists of comprehensive information about experimentally verified linear B-cell epitopes and tools for mapping these epitopes on an antigen sequence. In case query antigen contains known epitopes, this database might aid in the wet experimentation and lower the cost by reducing the overlapping repeats. This strategy is frequently used for the screening of transgenic proteins by searching linear IgE-binding epitopes 22. Unlike discontinuous epitopes, the linear epitopes are easy to design, as they do not require tertiary structure information. Bcipep also provides information on neutralizing B-cell epitopes where an antibody generated against a B-cell epitope neutralizes the parent antigen. The current version of Bcipep provides neutralizing information on about 1309 such B-cell epitopes. This information is very important for selecting functional B-cell epitopes. This database also provides a link with MHCBN to search for overlapping regions of MHC binders and T-cell epitopes in the B-cell epitopes. Thus, the user can identify both antigenic regions that can activate B-cell and T-cell, which can lead to the development of better vaccine. The epitopes in Bcipep can be used to derive the rules for predicting B-cell epitopes.

The aim of designing synthetic linear peptides as epitope-vaccine is to induce neutralizing antibodies against the pathogen 23. There are many reports that the linear B-cell epitopes were characterized as neutralizing antibodies as in Clostridium botulinum neurotoxin type A (Btx A)24. In Bcipep, there are 748 neutralizing anti-peptide antibodies entries. However, in some cases these linear epitope(s) fail to produce neutralizing antibodies and do not give protective immunity. For instance, it has been shown in the past that the antibodies against the synthetic peptides and short recombinant proteins of approximately 100 amino acids of hepatitis E virus (HEV) do not neutralize, suggesting that the HEV neutralization epitope(s) is conformation dependent 25. The elicitation of a bactericidal and protective immune response to Borrelia burgdoferi decorin binding protein requires a properly folded conformation for the production of functional antibodies 26. Recently, Corcoran et al, 2004, observed that B-cell memory is established and maintained against conformational epitopes of Parvovirus VP2 and against linear epitopes of VP1 but not against linear epitope VP2 27. Thus, it is not necessary that the linear B-cell epitope will always give rise to memory cells. One should also check the neutralizing information of B-epitopes, as only 748 B-cell epitopes out of 1309 in Bcipep were able to neutralize the parent protein.

For an effective use of Bcipep, it is important to understand the limitation of linear B-cell epitopes and data in Bcipep. The few limitations of current version of Bcipep are; i) it does not cover discontinuous epitopes, ii) it has limited number of unique peptides (1590) in 3031 entries and, iii) it contains peptides having only natural amino acids. One should be careful in using linear B-cell epitopes in developing epitope based subunit vaccine. The organism used for immunization (information included in the database) should also be taken into consideration, since immune response is T-helper cell (MHC-II-peptide complex) dependant and B-cell epitope alone may not generate protective antibodies 28. In some cases, the nature of the adjuvant used and the route of immunization (information not included in the database) might also play important roles in the induction of protective anti-peptide antibody response against the pathogen 293031.

SS collected and compiled the data as well as developed the web server. MB helped in designing website and stored data in PostgreSQL. GPSR conceived the idea and supervised the work.