Related Links
Immunological Databases:-

    This is a comprehensive database of MHC binding and Non binding peptides. The entries were complied from literature and public databases. The current version of database is consist of 20989 enteries.The database is crosslinked to SWISS-PROT, PDB,GenBank and NCBI.The database have a set of data extraction and analysis tools. The mirror site of the database is available at http://bioinformatics.uams.edu/mirror/mhcbn/

    SRS versions of MHCBN:-

  • BCIPEP

    BCIPEP is consist of B cell epitopes of varying immunogenicity. The current version of database is consist of 552 peptides interacting B cells.The enteries of the database are hyperlinked to NCBI,SWISS-PROT and GenBank.

  • JenPep

    JenPep, is a database containing quantitative binding data for peptides binding to MHC class I, II and TAP molecules. JenPep also contains a separate T cell epitope database. All entries are from published experimentally determined data. The Version 1.1 of database contains more than 8000 entries.

  • MHCPEP

    MHCPEP is a database comprising over 13000 peptide sequences known to bind MHC molecules. Entries were compiled from published reports as well as from direct submissions of experimental data.

  • SYFPEITHI

    The database comprising approximately 3500 peptide sequences known to bind class I and class II MHC molecules. The entries are compiled from published reports only.

  • HIV Molecular Immunology Database

    The HIV Molecular Immunology Database is an annotated, searchable collection of HIV-1 cytotoxic and helper T-cell epitopes and antibody binding sites.The database is also having the epitope map of every HIV protein.

  • FIMM

    FIMM is an integrated database of functional immunology, focusing on MHC, antigens, and diseases.

  • IMGT

    IMGT, the international ImMunoGeneTics project, is a collection of high-quality integrated databases specialising in Immunoglobulins, T cell receptors and the Major Histocompatibility Complex (MHC) of all vertebrate species.IMGT/LIGM is a comprehensive database of fully annotated sequences of Immunoglobulins and T cell receptors from human and other vertebrates.IMGT/HLA is a database for sequences of the human MHC, referred to as HLA.IMGT/MHC a centralised repository for sequences of the major histocompatibilty complex from a number of different species.

MHC Binders & T epitope Prediction Methods:-

    This is a comprehensive method for prediction of MHC binding peptides or CTL epitopes of 67 MHC alleles.The prediction for 30 alleles is based on the hybrid appoarch of Artificial Neural Networks (ANNs) and Quantitative Matrices (QM). The prediction for rest 37 MHC alleles is based on the quantiatative matrices.The predicted MHC binders are filtered to potential CTL epitopes by using Proteasomal matrices.

    The ProPred-I is an on-line service for identifying the MHC Class-I binding regions in antigens. It implements matrices for 47 MHC Class-I alleles,proteasomal and immunoproteasomal models. The main aim of this server is to help users in identifying the promiscuous regions.

    The method predict 8-mer, 9-mer, or 10-mer peptides based on a predicted half-time of dissociation to HLA class I molecules. The analysis is based on coefficient tables deduced from the published literature by Dr. Kenneth Parker.

    MAPPP (MHC-I Antigenic Peptide Processing Prediction) will predict possible antigenic peptides to be processed and finally presented on the cell surfaces. It aides the prediction of immunodominant T-cell epitopes.

    The methods allows you to find out theligation strength to a defined HLA type for a sequence of aminoacids. The algorithmus used are based on the book "MHC Ligands and Peptide Motifs" by H.G.Rammensee, J.Bachmann and S.Stevanovic. The probability of being processed and presented is given in order to predict T-cell epitopes.

    This program ranks all possible peptides from an input protein sequence/s by their similarity to a set of peptides known to bind to a given MHC molecule. Similarity is scored using a Position Specific Scoring Matrix (PSSM) built from a collection of aligned peptides known to bind to that MHC molecule.

    This is a structure-based algorithm for prediction of MHC class I epitopes .

    .The server will predict mutated promiciuous and gigh affinity mutated MHC class-I binding peptides in any antigenic protein. The prediction is based upon quantitative matrices derived by extracting the data from MHCBN database. The server can run prediction for 47 MHC class I alleles.

    The server will predict MHC Class-II binding regions in an antigen sequence, using quantitative matrices derived from published literature by Sturniolo et. al., 1999. The server will assist in locating promiscuous binding regions that are useful in selecting vaccine candidates.

    The server predict the MHC class II restricted T cell epitopes . The prediction is based on the quantitative matrices.

    Predict is the interface for prediction of peptide binding to Major Histocompatibility Complex (MHC) molecule. This interface uses the artificial neural network models, hidden markov's model or motifs for predictions of peptide binders to various MHC models (system or user-created).The demo version of this server is only present.

  • TEPITOPE

    • This is a software for the prediction of MHC calss II restricted promiscuous T cell epitopes or vaccine candidates.The prediction is based on the virtual matrices derived by Sturniolo et. al., 1999.

    The prediction of T cell epitopes is based on MHC binding motif density and AMPHI algorithm.

    This is a MHC class I binding peptide prediction method. The prediction is based on the Support Vector Machine.

Proteasome Prediction:-

    The server predict cleavage site of human and yeast 20S proteasomes in the query sequence.The prediction is based on the artificial neural networks.

    The server predict cleavage site of human proteasomes in the query sequence.The prediction is based on the artificial neural networks.

Commercial Organizations for Epitope Prediction:-
  • Epitope-Informatics: 

    The ePitope Informatics is an Internet-based, applied bioinformatics company of Professors, providing a range of services for the prediction and analysis of protein epitopes (B cell). The company also deals in the commercial antibody production and synthesis of peptides.

  • EpiVax: 

    EpiVax is dedicated to merging in vitro immunology research with bioinformatics to generate new vaccines for infectious diseases such as HIV, TB, and hepatitis, new therapeutics for cancer and auto-immune diseases, and new diagnostics for organ and marrow transplantation.

  • Cambridge Research Biochemicals Limited: 

    This is a commercial company for synthesis of peptide and antibodies for the research in biology.

  • Epimmune deals with the synthesis and testing of T cell epitopes.The Company has four proprietary technology platforms related to the discovery and validation of epitopes (fragments of antigens) that fuel internal drug development programs and provide a range of licensing and partnering opportunities.