BciPep a database of B cell epitopes

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.

Entry No::This is a five digit unique identifier provided to each entry of the database.The entries can be serched from the database by using this unique identifier.
Peptide Sequence::This field have the amino acid sequence of the immunogenic peptide.The sequence is stored in the single amino acid code.
Source Protein::The field contain the information about the protein from which the antigenic peptide is derived. The field also provide the specific information about the position of the peptide in the antigenic sequence.
Pathogen Group::The field the group of the organism to which the source protein or antigen belongs.The majors antigenic groups are bacteria,fungi,virus
Database Reference:: All peptides of the database has been searched in the SWISS-PROT database to extract the proteins having matching peptides.The Swiss-Prot codes of proteins having matching peptides were stored in database reference field of each entry.The summary of these proteins stored locally and provided with hypertext links to SWISS-PROT and GenBank to provide more detailed information.The database have sequences of 10700 antigenic proteins.
Antigen Structure:: All peptides of the database has been searched in the PDBaa database (available for BLAST) to extract the proteins having matching peptides.The PDBaa contains the primary sequence of all proteins whose tertiary structure is available.The PDB codes of proteins having matching peptides were stored in Antigenic Structure field of each entry.The summary of these proteins stored locally and provided with hypertext link PDB for more detailed information.The database have structure of 1216 antigenic proteins.
Antibody::This field contain the information about the antibodies which are produced or specific to test peptide. The antibody may be specific or non specific. They are checked mostly by two methods one is ELISA and another one is using whole sera for antibody production.This give an idea about the type of immune response generated by the peptide.
Experimental Method::This field of each entry specify the experimental method which are used for checking the immunogenic or antigenic properties of the peptide.
Model Organism::This field have information about the organism which is used for checking the immunogenic properties of the peptide in vivo.Most of time inbred mice are used as animal model.

Measure of Immunogenicity::This is semiquantitative measure of immunogenic activity of the peptide.The is calculated by measuring the effect of peptide on the antibody production.The different level of immunogenicity are described through this table.

Term	Description
Immunodomiant	The peptide which result in 2-3 fold increase in anti-peptide antibodies in comparision to reference or control peptide and produce protective immunity.
Immunogenicity	The peptide which result in 1 fold increase in anti-peptide antibodies in comparision to reference or control peptide and produce immunity.
Null Immunogenicity	The peptide which result inbase level of antibody production as produced by control peptide.

Publication reference::This field have the published reference of peptide in the coded form.The first of code specify the first author sirname. The next two digits specify the year of publication.The next word after underscore denotes the journal name.The last digits after second underscore denotes stating page of published reference.
The deciphacialed publiaction reference: first author of paper along with last two digits of year of publication_journal code_first page of published reference.
This is field is internally linked to flat files which is further hyperlinked to NCBI.

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: webs.iiitd.edu.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://webs.iiitd.edu.in/raghava/bcipep.

Copyright

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