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Dr. G. P. S. Raghava
Bioinformatic Centre
IMTECH, INDIA

       
 

Introduction:-Bcipep is collection of the peptides having the role in Humoral immunity. The peptides in the database has varying measure of immunogenicity.This database can assist in the development of method for predicting B cell epitopes, desigining synthetic vaccines and in disease diagnosis. These peptide leads to the generation of the antibodies which combine with the antigen and responsible for the host defence. These peptide can be very useful for subunit vaccine designing. The database is having 3031 peptide enteries. The each entry of the database provide following information.




Schematic diagram of B-cell epitope



Statistics on "pathogen group' and 'immunogenicity' vice distribution of B cell epitopes in the database

Pathogen  Immunodominant   Immunogenic  Non-immunogenic
Virus     (2046)         415         1474      157
Bacteria (539)         130          159        250
Protozoa (236)          139            57        40
Fungi      (53)         17            23        15
Others (157)         62           84         9


Application of Bcipep data in prediction methods

The Physio-chemical properties of amino acids in B-cell epitope can be identified e.g., Hydrophilicity, flexibility, accessibility, turns and tested on this experimental determined epitopes.

        Seq =AAAHHGSTEERENANPNANPNANPGFGFERRWEQSADADHGFGFDWERWNANPNANPDSF

Diagram showing Hydrophilicity scale on Y axis and amino acids in the x axis.

The amino acids in the protein above the threshold value (>2) of a physio-chemical scale (eg., Hydrophilicity ) can be predicted as B-cell epitope. Bcipep can be helpful in determining threshold value, analysis and validation of the existing methods for the prediction of B-cell epitope. New method(s) can be used like machine learning language which can differentiate between epitope and non-epitope.

B-cell epitopes obtained from this database (Bcipep) have been used for evaluation of prediction methods of continuous B-cell epitopes in antigenic sequences using physico-chemicalproperties.

see the website:
BcePred: www.imtech.res.in/raghava/bcepred/

Reference: Saha.S and G.P.S.Raghava. BcePred:Prediction of Continuous B-cell Epitopes In Antigenic Sequences using physico-chemical Properties. In G.Nicosia,V.Cutello,P.J.Bentley and J.Timmis(Eds.) ICARIS 2004, LNCS 3239, pp. 197-204, Springer,2004.



Bcipep data mangement

All data in Bcipep has been maintained in "Relational Database Management System" (RDBMS) called PostgreSQL which is a public domain software freely available to public. Full information about a peptide has been stored in a single table. Related information like publication reference and source proteins reference has been stored in directories having internal links to main database.

Specification for Access of Bcipep

The Bcipep web server was developed in a UNIX environment on SUN server 420E in Solaris 7.0. This server is designed to provide easy access to the user, based upon a set of simple GUI (Graphical User Interface) forms. Methods for searching the databases and displaying the selected objects were built with a combination of HTML, CGI-scripts in PERL 5.4.



Requirements for accessing Bcipep on your system
    • Windows 95 and above for personel computers
    • Internet Explorer 4.01 and above/Netscape 3.01 and above

Best view of Bcipep can be observer with
    • a 1024x768 screen
    • not to override the web pages with your windows default colors.
    • to set font size of browser at 12 (Helvetica) or medium.


Submission and Updation of Bcipep:-

The web server allows user to submit their peptide on-line by filling a HTML form. However, before including in Bcipep we will confirm the validity of the peptide, in order to maintain the quality. Our team is also searching and adding the peptides in database from published literature.

In order to maintain the consistency we will release bcipep database twice per year. All peptide obtain during two release will be available as new submissions.



Citing Bcipep:-

Authors making use of the information provided in this database should cite this article as a general reference and quote BCIPEP home page URL http://www.imtech.res.in/raghava/bcipep.



Copyright

 
© Copyright 2003; Bcipep: A Database of Immunodominant B cell Epitopes