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Bcipep: a database of B-cell epitopes.

Saha S, Bhasin M, Raghava GP - BMC Genomics (2005)

Bottom Line: A comprehensive database of B-cell epitopes called Bcipep has been developed that covers information on epitopes from a wide range of pathogens.The Bcipep will be source of information for investigators involved in peptide-based vaccine design, disease diagnosis and research in allergy.It should also be a promising data source for the development and evaluation of methods for prediction of B-cell epitopes.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute of Microbial Technology Chandigarh, India. saha@imtech.res.in <saha@imtech.res.in>

ABSTRACT

Background: Bcipep is a database of experimentally determined linear B-cell epitopes of varying immunogenicity collected from literature and other publicly available databases.

Results: The current version of Bcipep database contains 3031 entries that include 763 immunodominant, 1797 immunogenic and 471 -immunogenic epitopes. It covers a wide range of pathogenic organisms like viruses, bacteria, protozoa, and fungi. The database provides a set of tools for the analysis and extraction of data that includes keyword search, peptide mapping and BLAST search. It also provides hyperlinks to various databases such as GenBank, PDB, SWISS-PROT and MHCBN.

Conclusion: A comprehensive database of B-cell epitopes called Bcipep has been developed that covers information on epitopes from a wide range of pathogens. The Bcipep will be source of information for investigators involved in peptide-based vaccine design, disease diagnosis and research in allergy. It should also be a promising data source for the development and evaluation of methods for prediction of B-cell epitopes. The database is available at http://www.imtech.res.in/raghava/bcipep.

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Related in: MedlinePlus

Mapping of peptide in MHCBN database; a) mapping of MHCBN peptides on B-cell epitope, and b) full information about a MHCBN peptide.
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Figure 4: Mapping of peptide in MHCBN database; a) mapping of MHCBN peptides on B-cell epitope, and b) full information about a MHCBN peptide.

Mentions: This server allows searching of peptide in Bcipep against MHCBN database. The MHCBN database provides information about components of cell-mediated immunity like MHC binders/non-binders, T-cell epitopes and TAP binders [14]. The peptides related to cell-mediated immunity can be mapped on resultant B-cell epitopes obtained from keyword/peptide search by clicking on 'Peptide Sequence' field (Figures 2b and 3b). Thus, the server is useful in identifying the potential B-cell epitopes having T-cell epitopes (or MHC binders). The example of mapping of MHCBN peptides on B-cell epitope (by clicking on peptides sequence field of Figure 3b) is shown in Figure 4a. The full information of each map peptide can be obtained by clicking on the mapped sequence. One such example is shown in Figure 4a and 4b. The mapping allows user to detect the regions in B-cell epitope having promiscuous MHC binders (peptides that can bind to large number of MHC alleles) or T-cell epitopes.


Bcipep: a database of B-cell epitopes.

Saha S, Bhasin M, Raghava GP - BMC Genomics (2005)

Mapping of peptide in MHCBN database; a) mapping of MHCBN peptides on B-cell epitope, and b) full information about a MHCBN peptide.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC1173103&req=5

Figure 4: Mapping of peptide in MHCBN database; a) mapping of MHCBN peptides on B-cell epitope, and b) full information about a MHCBN peptide.
Mentions: This server allows searching of peptide in Bcipep against MHCBN database. The MHCBN database provides information about components of cell-mediated immunity like MHC binders/non-binders, T-cell epitopes and TAP binders [14]. The peptides related to cell-mediated immunity can be mapped on resultant B-cell epitopes obtained from keyword/peptide search by clicking on 'Peptide Sequence' field (Figures 2b and 3b). Thus, the server is useful in identifying the potential B-cell epitopes having T-cell epitopes (or MHC binders). The example of mapping of MHCBN peptides on B-cell epitope (by clicking on peptides sequence field of Figure 3b) is shown in Figure 4a. The full information of each map peptide can be obtained by clicking on the mapped sequence. One such example is shown in Figure 4a and 4b. The mapping allows user to detect the regions in B-cell epitope having promiscuous MHC binders (peptides that can bind to large number of MHC alleles) or T-cell epitopes.

Bottom Line: A comprehensive database of B-cell epitopes called Bcipep has been developed that covers information on epitopes from a wide range of pathogens.The Bcipep will be source of information for investigators involved in peptide-based vaccine design, disease diagnosis and research in allergy.It should also be a promising data source for the development and evaluation of methods for prediction of B-cell epitopes.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute of Microbial Technology Chandigarh, India. saha@imtech.res.in <saha@imtech.res.in>

ABSTRACT

Background: Bcipep is a database of experimentally determined linear B-cell epitopes of varying immunogenicity collected from literature and other publicly available databases.

Results: The current version of Bcipep database contains 3031 entries that include 763 immunodominant, 1797 immunogenic and 471 -immunogenic epitopes. It covers a wide range of pathogenic organisms like viruses, bacteria, protozoa, and fungi. The database provides a set of tools for the analysis and extraction of data that includes keyword search, peptide mapping and BLAST search. It also provides hyperlinks to various databases such as GenBank, PDB, SWISS-PROT and MHCBN.

Conclusion: A comprehensive database of B-cell epitopes called Bcipep has been developed that covers information on epitopes from a wide range of pathogens. The Bcipep will be source of information for investigators involved in peptide-based vaccine design, disease diagnosis and research in allergy. It should also be a promising data source for the development and evaluation of methods for prediction of B-cell epitopes. The database is available at http://www.imtech.res.in/raghava/bcipep.

Show MeSH
Related in: MedlinePlus