MHCBN consists of ~25860 MHC binding and non-binding peptides and ~1052.5 peptides interacting with TAP. The database is cross-linked to NCBI, Swiss-Prot, PDB, OMIM and GenBank.
 
 

Contents

Architecture of MHCBN Database  [table of contents]
 

 

Recent Development at MHCBN  [table of contents]

 
This is Version 4.0 of MHCBN database. Following data is available at MHCBN
AUGUST, 2006: Version 4.0
  Peptide Entries in MHCBN (25852)
    • 20717 MHC Binders
    • 4022 MHC non-binders
    • 1053 TAP binders and non-binders
    • 6722 T-cell epitopes
    • Unique Peptides (non-redundant peptides) in Database (13910)
    •  12722 MHC binding peptides
    •  1566 MHC non-binding peptides
    •  4907 T-cell epitopes
    • 470 TAP binders and non-binders
      • Unique Peptides having matching peptide in Proteins/Antigens (6408)
    • 5876 Binders
    • 953 Non-binders
    • 2602 T-cell epitopes
    • 126 TAP interacting peptides
    Misc. Data in MHCBN Database
        • 1420 Proteins of MHC alleles
        • 3754 Protein sequence having matching peptide
        • 1519 References (Published Litrature)
        • 841 Protein Structure having matching peptide
        • 119 MHC related Protein Structures


For full detail visit web page ?Statistical Analysis?


 

Aims & Objectives  [table of contents]

The main aim of this database is to serve the academic community working in field of subunit or DNA vaccine designing. This is a comprehensive database provides information about most of MHC binders, MHC non-binder,TAP binders, TAP non-binders and T-cell epitopes reported in literature. The peptide information is essential to develope methods for predicting MHC binders, non-binders and T-cell epitope.

The database have number of web tools which allow one to I) search any information about MHC alleles and peptides ii) mapping of experimentally determined MHC binders,MHC non-binders and T-cell epitopes peptides in query protein sequence; iii) BLAST search against related antigenic proteins and MHC associated proteins; and iv)


 

Data Mangement at MHCBN  [table of contents]

All data in MHCBN 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 reference, source proteins, MHC proteins has been stored in directories with internal links to main database.

 
Table 1. MHCBN Main Table
 
Field Name  Full Description of Field
Entry No. Each Entry has a unique number called identifier
sequence Consists of single letter code of amino acid sequence as reported.
Anchor Position The numerical position of anchor amino acid in peptide from N-terminal. 
Antigenic Structure This field contain PDB code of  proteins  having matching peptides in sequence. 
Binding affinity measure of binding affinity of peptide &MHC which is mostly determined by IC50 Value.
comment Additional information about particular entry
Database Reference consists SWISSPROT code of   proteins having matching peptide sequence.
Host organism Provides the name of  host in which specfic MHC allele is occuring (eg Human, Mouse, Monkey, Chimpanzee etc)
MHC Allele  Commonly used name of MHC protein
MHC Classes Provides the class of MHC molecule (Class I or Class II)
MHC structure Consists the PDB Code of MHC protein or similar protein. 
Expeimental Method Describe the method used for studying immunological properties of peptides.
Publication Reference This field consists reference code of published litrature from where peptide were obtained.It is consisit of author name and year of publication.
Source Protein This field consists antigenic proteins with exact location of peptide 
T-cell Activity semi-Quantitive measure of immunogenic potency of peptide. 

 

Internal Links

  • Publication Reference: The server consists brief information (e.g. title, years, name of journal and authors of paper) of source of entry which is link with ' Publication Reference' field of database.
  • Database Reference: Protein sequences having matching peptide are available at our server in FASTA format with link to 'Database Reference' field.
  • MHC Allele sequence: The sequence of Most of MHC alleles are stored at our sever. The server provide Exact and Apporaximate search on MHC seauence database.
  • Structures of MHC proteins:  All the MHC protein and related protein structure are stored at our server with link to field  'MHC structure'
  • Structure of Antigenic proteins: The MHCBN server consists summary of protein structure having matching peptide in its amino acid sequence  with link to field 'Antigenic Structure'.

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External Links
  • Sequence Databases: This server contain amino acid sequence of antigenic proteins in FASTA format for further information these sequences have hypertext linked with  'NCBI ENTREZ' and 'SWISSPROT' database.
  • Structure Database:  All the structure of protein have hyper text linked to PDB database.
  • MHC Database: In order to provide detail information about sequence MHC alleles , we linked MHC protein sequence with 'IMGT/HLA-DB' and 'NCBI ENTREZ' database.
  • Medline Databse: The MHCBN consists brief information (e.g. title, years, name of journal and authors of paper), and hypertext link to PubMed at NCBI.

 

System Requirement for Access[table of contents]

The MHCBN 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 Java Scripts, CGI-scripts in PERL 5.4.

System requirements for running the MHCBN System are :
    • For PC, Windows 95 and above
    • Internet Explorer 4.01 and above/Netscape 3.01 and above
    • Java-Scripts
For best view, the MHCBN System requires :
    • a 1024x768 screen
    • not to override the web pages with your windows default colors.
    • to set font size of browser at 14 (Helvetica) or medium.

 

Data Submission and Updates  [table of contents]

The web server allows user to submit their peptide on-line by filling a HTML form. However, before including in MHCBN 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 MHCBN database quaterly. All peptide obtain during two release will be available as new submissions. The success of this database is highly depend upon contributor, please enter the peptide in MHCBN or inform our team so that we can include more and more peptide in database.
 
 


 

Acknowledgements [table of contents]

We use the following public domain programs in MHCBN:

 

Disclaimer and Limitation of Liability[table of contents]

Data, information, e-mail addresses , hyperlinks (URLs) and data analysis tools provided by BIC, IMTECH New Delhi are on an "as is" basis, without any warranties. IMTECH and the developers of MHCBN give no warranty, including without limitation to the quality, accuracy or completeness of data or information, or that the use of data or information or data analysis tools will not infringe any patent, or intellectual property rights of any party. IMTECH shall not be liable for any claim, including without limitation, for any kind of loss, harm, illness, damage, injury originating from access to or use of data, information, e-mail addresses, hyperlinks (URLs) and data analysis tools, even if IMTECH advises of the possibility of such damages.


 

Copyright  [table of contents]

Copyright 2003; MHCBN: A comprehensive database of MHC binders, Non-binders and T-cell epitopes

Last updated on August, 2006,