The IMGT Immunoinformatics page

The IMGT Immunoinformatics page comprises links to databases, tools and resources on immunoglobulins (IG) or antibodies, T cell receptors (TR) and major histocompatibility complex (MHC).

Editors: Marie-Paule Lefranc and Gérard Lefranc pdf (LIGM, Université Montpellier 2, CNRS, Montpellier, France)

Databases
Tools
- IG
- TR
- MHC
- Peptides binding to MHC
- Allergens
Resources
Nobel lectures
Documentation
IMGT posters and diaporama
Meeting announcements
Networks

More information:

Immunology themes (IMGT Bloc-notes) for links to immunology web sites by themes in alphabetical order (allergy, allergens, etc.)
Immunology (IMGT Education)
Interesting links (IMGT Bloc-notes)

Databases

Immunoglobulins (or Antibodies) (IG)
- IMGT/LIGM-DB, a comprehensive database of germline and rearranged immunoglobulin and T cell receptor genes from human and other vertebrates, with translation for fully annotated sequences, LIGM, CNRS, Université Montpellier 2, Montpellier, France.
- IMGT/3Dstructure-DB, IMGT gene and allele identification and Collier de Perles of PDB structural data.
- IMGT/PRIMER-DB
- Kabat database, sequences of Proteins of Immunological Interest, Rel.15.0, contains 5th edition April 1991 (ftp).
- ExactAntigen, for search of commercial, academic, and therapeutical monoclonal antibodies.
T cell receptors (TR)
- IMGT/LIGM-DB, a comprehensive database of germline and rearranged immunoglobulin and T cell receptor genes from human and other vertebrates, with translation for fully annotated sequences, LIGM, CNRS, Université Montpellier 2, Montpellier, France.
- IMGT/3Dstructure-DB, IMGT gene and allele identification and Collier de Perles of PDB structural data.
- IMGT/PRIMER-DB
- Kabat database, sequences of Proteins of Immunological Interest, available only by paid subscription.
Major histocompatibility complex (MHC)
- Bovine Leucocyte Antigens (BoLA) Nomenclature Committee Web Site
- Complete Human MHC Sequence at the Sanger Centre, UK
- HLA Database, at Cancer Vaccine Center. The data used in this database has been drawn from the IMGT/HLA database.
- IMGT/3Dstructure-DB, IMGT gene and allele identification of structural data, IMGT Collier de Perles, IMGT reference pMHC contact sites, TR/pMHC interactions
- IMGT/MHC-DB, at EBI, UK, which comprises sequence databases of human MHC or HLA (IMGT/MHC-HLA), MHC from non human primates (IMGT/MHC-NHP), canines and felines (IMGT/MHC-DLA) and felines (IMGT/MHC-FLA). NAR 2003
- MPID-T, MHC-Peptide Interaction Database
- The MHC Haplotype Project at the Sanger Center, UK
Antigens
- Peptides binding to MHC
  - AntiJen, an extension of JenPep, a database of quantitative binding data for peptide binding molecules, immunological protein-protein interactions and peptide libraries.
  - EPIMHC, a curated database of MHC ligands
  - EpiPox Database, at Cancer Vaccine Center. The data used in this database has been drawn from the Poxvirus Bioinformatics Resource Center database
  - JenPep, Peptide Binding Database, a database containing quantitative binding data for peptides binding to MHC class I, II and TAP molecules. JenPep also contains a T cell epitope and B cell epitope database. All entries are from published experimentally determined data.
  - MHCBN, a database of MHC binding and non-binding peptides and T cell epitopes.
  - MPID-T, MHC/peptide interaction database
  - SiPeP (SNPs in Peptides/Proteins), a database of nonsynonymous coding SNPs (Single Nucleotide Polymorphisms) obtained from dbSNP, with matrix and molecular dynamic scoring data for binding of these peptides with available MHC alleles.
  - SNPBinder, a database of predicted minor histocompatibility antigens (mHAgs) and antigenic peptides.
  - SYFPEITHI, a database of MHC ligands and peptide motifs. For MHC ligands, only contains peptides that have been eluted from MHC and sequenced by Edman degradation or mass spectrometry.
- Antigens eliciting an antibody response
  - AntiJen, an extension of JenPep, a database of quantitative binding data for peptide binding molecules, immunological protein-protein interactions and peptide libraries.
  - Bcipep, a database of immunant dominant B cell epitopes.
  - CIDB, Cancer Immunome Database, repertoire of antigens eliciting an antibody response in cancer patients (CIDB is an updated version of SEREX), the serological identification of antigens by recombinant expression cloning (need registration).
  - JenPep, Peptide Binding Database, a database containing quantitative binding data for peptides binding to MHC class I, II and TAP molecules. JenPep also contains a T cell epitope and B cell epitope database. All entries are from published experimentally determined data.
  - Platelet glycoprotein antigens (human)
- Allergens
  - ALLERDB
  - Allergen Nomenclature, International Union of Immunological Societies (IUIS). Allergen Nomenclature Sub-Committee
  - Farrp Allergen Database (needs registration)
  - Food Allergen Sequences. The Biotechnology Information for Food Safety (BIFS) Database.
  - InformAll Database. Communicating about Food Allergies. Contains data from previous Protall Database, food allergens of plant origin
  - Nomenclature and index of allergen sequences, Swiss-Prot
  - SDAP, Structural Database of Allergenic Proteins
  - The Allergen Database (adb) at CSL, allergen epitopes (needs registration)
- Epitopes
  - Epitome, a database of structure-inferred antigenic residues in antigen/antibody complex structure
  - CED, a conformational epitope database
  - IEDB, The Immune Epitope Database and Analysis Resource
- Haptens
  - HaptenDB, a database of haptens, carrier proteins and anti-hapten antibodies
KIR
- KIR database
Peptides with antimicrobial activity or antibiotic peptides
- AMSDb, Antimicrobial Sequences Database
- APD: the Antimicrobial Peptide Database
- BACTIBASE Database, a data repository of bacteriocin natural antimicrobial peptides
- Cybase, a database of cyclic peptides and proteins (or cyclotides)
- Defensins Knowledgebase
- PenBase, Penaeidin database, curated database of antimicrobial peptides from penaeid shrimps
- Peptaibol Database, a database of peptaibols, antimicrobial peptides with non-standard amino acids, mainly from fungii (Trichoderma, Emericellopsis)
- PhytAMP, a database dedicated to antimicrobial plant peptides
- The KNOTTIN database
Immunodeficiency
- Immunodeficiency Mutation Databases (IDbases), databases for immunodeficiency-causing mutations, University of Tampere, Finland
Innate immunity genes
- ImmunomeBase: A database for metazoan immunity genes and orthologs.
- IRIS, Immunogenetic Related Information Source

Tools

Immunoglobulins (or Antibodies) (IG)
- Gene and allele identification - Analysis of the V-J and V-D-J junction
  - IMGT/V-QUEST sequence alignment software and IMGT Collier de Perles for V-DOMAIN.
  - JoinSolver®
  - VDJsolver
- Analysis of the V-J and V-D-J junction
  - IMGT/JunctionAnalysis
- Gene identification
  - IgBLAST
  - SoDa, Somatic Diversification Analysis (requires e-mail).
  - VBase/DNAPlot
- Phylogeny
  - IMGT/Phylogene
- Sequence comparison
  - IMGT/Allele-Align
  - iHMMune-align, a HMM-based Partitioning Utility for the Human Immunoglobulin Heavy Chain.
  - VBASE2
- 3D Structures
  - IMGT Collier de Perles
  - IMGT/DomainDisplay
  - IMGT/DomainGapAlign
  - IMGT/DomainSuperimpose
  - IMGT/StructuralQuery allows to retrieve IMGT/3Dstructure-DB entries according to domain and/or position criteria, using the IMGT unique numbering for V-DOMAIN and C-DOMAIN
- Modelisation
  - WAM - Web Antibody Modelling, uses the same algorithm as its commercial homolog "AbM".
T cell receptors (TR)
- Gene and allele identification - Analysis of the V-J and V-D-J junction
  - IMGT/V-QUEST sequence alignment software and IMGT Collier de Perles for V-DOMAIN.
- Analysis of the V-J and V-D-J junction
  - IMGT/JunctionAnalysis
- Gene identification
  - SoDa, Somatic Diversification Analysis (requires e-mail)
- Phylogeny
  - IMGT/Phylogene
- Sequence comparison
  - IMGT/Allele-Align
- 3D Structures
  - IMGT Collier de Perles
  - IMGT/DomainDisplay
  - IMGT/DomainGapAlign
  - IMGT/DomainSuperimpose
  - IMGT/StructuralQuery allows to retrieve IMGT/3Dstructure-DB entries according to domain and/or position criteria, , using the IMGT unique numbering for V-DOMAIN and C-DOMAIN
Major histocompatibility complex (MHC)
- Sequence comparison
  - Polymorphism search tool, for HLA sequence polymorphisms.
- 3D Structures
  - IMGT/StructuralQuery allows to retrieve IMGT/3Dstructure-DB entries according to domain and/or position criteria, using the IMGT unique numbering for G-DOMAIN
- Prediction of MHC I binding peptides
  - NetCTL, predicts CTL epitopes in protein sequences. NetCTL | Download software | SOAP WS NetMHCpan, predicts binding of peptides to 478 and 791 different HLA-A and HLA-B alleles using artificial neural networks (ANNs).
- Prediction of MHC II binding peptides
  - NetMHCII, predicts binding of peptides to a number of different HLA-DR alleles using position specific weight matrices (PSSM).
Peptides binding to MHC
- Prediction of proteasome cleavages
  - MAPPP, MHC-I Antigenic Peptide Processing Prediction, combined proteasome cleavage and MHC ligand prediction.
  - NetChop Prediction Server, produces neural network predictions for cleavage sites of the human proteasome.
  - PAProC, Prediction Algorithm for Proteasomal Cleavages
- Prediction of MHC I binding peptides
  - CombiPRED, a matrix-based MHC Class I prediction tool that combines MHC allele matrices from three MHC prediction programs - nHLAPred, BIMAS and SYFPEITHI, part of a pipeline of tools for vaccine design applied to bacteria.
  - CTLPred, a SVM and ANN based CTL epitope prediction.
  - HLA Peptide Binding Predictions, Bioinformatics and Molecular Analysis Section (BIMAS), a method based on profiles and predicted half-time of dissociation of a given MHC class I - peptide complex.
  - MHCPred, quantitative prediction of peptide-MHC binding.
  - NetMHC, prediction of peptide binding to HLA alleles using artificial neural networks (ANNs) and hidden Markov models (HMMs).
  - nHLAPred, a neural network based MHC Class-I Binding Peptide Prediction Server.
  - PREDEP, MHC Class I epitope prediction (see Resources).
  - ProPred-I, the Promiscuous MHC Class-I Binding Peptide Prediction Server.
  - RANKPEP, prediction of binding peptides to MHC (class I and class II) molecules.
  - SMM, prediction of high affinity HLA-A2-binding peptides, based on an matrix-based algorithm.
  - SNEP, single nucleotide polymorphism (SNP)-derived Epitope Prediction program for minor histocompatibility antigens (miHAgs), at the Department of Immunology, University of Tuebingen, Germany.
  - SVMHC, a machine learning method based on the support vector machine package SVM-light.
  - SYFPEITHI T cell epitope prediction, a method based on profiles.
- Prediction of MHC II binding peptides
  - EPIPREDICT, prediction of HLA-class II restricted T cell epitopes and ligands.
  - ProPred, MHC Class-II Binding Peptide Prediction Server, uses quantitative matrices.
  - RANKPEP, prediction of binding peptides to MHC (class I and class II) molecules.
  - SNEP, single nucleotide polymorphism (SNP)-derived Epitope Prediction program for minor histocompatibility antigens (miHAgs), at the Department of Immunology, University of Tuebingen, Germany.
- Mimicry probability and immunodominant profile
  - SEMANTICA:SEquence Minicry and ANTIgen Composition Analysis
- Commercial MHC prediction sites
  - EpiVax, using EpiMatrix. MHC class I and class II binding predictions for researchers working on vaccines and therapeutics for HIV and a range of other pathogens, a method based on statistical analysis techniques (frequency matrix).
Allergens
- Allermatch™ - Sequence comparison to allergenic proteins.

Resources

Immunoglobulins (or Antibodies) (IG)
- Antibody engineering (The IMGT Biotechnology page)
- Monoclonal antibodies with clinical indications (IMGT Repertoire)
- AAAAA, AHo's Amazing Atlas of Antibody Anatomy, maintained by Annemarie Honegger, Zurich University, Switzerland
- ABG: directory of 3D structures of antibodies (last update 2001).
- Antibodies and diseases
- Antibody Resource Page , links to information and sites related to antibody suppliers, immunology resources, news, books, advertising.
- ExactAntigen, for search of commercial, academic, and therapeutical monoclonal antibodies
- Humanization bY Design, a compilation of data on humanization of murine antibodies.
- IG chains and V-DOMAIN. IMGT unique numbering for immunoglobulin and T cell receptor variable domains and Ig superfamily V-like domains. Lefranc, M.-P. et al., Dev. Comp. Immunol., 27, 55-77 (2003) PMID: 12477501 with permission from Elsevier
- IG chains and C-DOMAIN. IMGT unique numbering for immunoglobulin and T cell receptor constant domains and Ig superfamily C-like domains. Lefranc, M.-P. et al., Dev. Comp. Immunol., 29, 185-203 (2005) PMID: 15572068 with permission from Elsevier
- IMGT Genes on the Ensembl Genome Browser
- IMGT Repertoire a resource on locus representations, germline genes and alleles, protein displays, two-dimensional representations designated as Colliers de Perles, and three-dimensional representations of immunoglobulins, T cell receptors and Major Histocompatibility Complex, LIGM, CNRS, Université Montpellier 2, Montpellier, France.
- Immunoglobulins and B cells | Immunoglobulines et lymphocytes B - Tutorials, IMGT Education, Marie-Paule Lefranc and Gérard Lefranc, LIGM, Montpellier, France.
- Immunoglobulins | Immunoglobulines - Questions and Answers, IMGT Education, Marie-Paule Lefranc and Gérard Lefranc, LIGM, Montpellier, France.
- Mike's Immunoglobulin Structure/Function
- Immunoglobulines ou anticorps - Pharmacorama
- Recombinant Antibody Pages, provided by Stefan Dübel, Heidelberg, links to webpages related to recombinant antibody technology.
- Rotating RasMol Images, Immunoglobulin domain
- The immunoglobulin kappa genes and the kappa locus of the mouse
T cell receptors (TR)
- IMGT Genes on the Ensembl Genome Browser
- IMGT Repertoire a resource on locus representations, germline genes and alleles, protein displays, two-dimensional representations designated as Colliers de Perles, and three-dimensional representations of immunoglobulins, T cell receptors and Major Histocompatibility Complex, LIGM, CNRS, Université Montpellier 2, Montpellier, France.
- T cells receptors and T cells | Récepteurs T et lymphocytes T, Tutorials, IMGT Education, Marie-Paule Lefranc and Gérard Lefranc, LIGM, Montpellier, France.
- T cells receptors | Récepteurs des cellules T, Questions and Answers, IMGT Education, Marie-Paule Lefranc and Gérard Lefranc, LIGM , Montpellier, France.
- TR chains and V-DOMAIN. IMGT unique numbering for immunoglobulin and T cell receptor variable domains and Ig superfamily V-like domains. Lefranc, M.-P. et al., Dev. Comp. Immunol., 27, 55-77 (2003) PMID: 12477501 with permission from Elsevier
- TR chains and C-DOMAIN. IMGT unique numbering for immunoglobulin and T cell receptor constant domains and Ig superfamily C-like domains. Lefranc, M.-P. et al., Dev. Comp. Immunol., 29, 185-203 (2005) PMID: 15572068 with permission from Elsevier
Major histocompatibility complex (MHC)
- Allele Frequencies in Worldwide Populations, a compilation of population studies developed by Dr Derek Middleton, UK.
- BMDW Bone Marrow Donors Worldwide
- dbMHC Alignment viewer, Probe/Primer, MHC Graphic View, IHWG Projects (Anthropology, Allele frequencies, NK Receptors...), NCBI, USA
- HLA cDNA clones, Gene Set Bank, RIKEN Bioresource center
- HLA Data Library - Japanese Population Data, JSHI, Japan
- HLA-related links, M. Tevfik Dorak
- IMGT Repertoire for MHC, Montpellier, France.
- Major histocompatibility complex | Complexe majeur d'histocompatibilité, Questions and answers, IMGT Education, Marie-Paule Lefranc and Gérard Lefranc, LIGM, Montpellier, France.
- Major histocompatibility complex | Complexe majeur d'histocompatibilité, Tutorials, IMGT Education, Marie-Paule Lefranc and Gérard Lefranc, LIGM, Montpellier, France.
- MHC chain and G-DOMAIN. IMGT unique numbering for MHC groove G-DOMAIN and MHC superfamily (MhcSF) G-LIKE-DOMAIN. Lefranc, M.-P. et al., Dev. Comp. Immunol., 29, 917-938 (2005) PMID: 15936075 with permission from Elsevier
- NMDP National Marrow Donor Program - HLA Resources
- Structure and Function of the Major Histocompatibility Complex (MHC) Proteins
- The major histocompatibility complex of the rat (RT1)
- The MHC Haplotype Project at the Sanger Center, UK
- IHWG International Histocompatibility Working Group
- The Molecular Immunology Foundation
- WMDA World Marrow Donor Association
Genomes
- Human Genome Browser Gateway, UCSC Genome Browser
- Ensembl Genome Browser, The Sanger Institute and EBI
- Human Genome Resources, NCBI
- IMGT Genes on the Ensembl Genome Browser
- Other links in
  - IMGT Bloc-notes Resources for the human genome
  - The IMGT Veterinary page for the genomes of domestic, model and wild life species
Antigens
- Antigens eliciting an antibody response
  - Human Protein Atlas, Swedish Human Proteome Resource (HPR) program
  - EU ProteomeBinders, A European Infrastructure of Ligand Binding Molecules against the Human Proteome
- Peptides binding to MHC
  - Prediction and analysis of protein epitopes
    - EpiMatrix. MHC class I and class II binding predictions for researchers working on vaccines and therapeutics for HIV and a range of other pathogens, a method based on statistical analysis techniques (frequency matrix).
    - ePitope informatics - Links
  - Prediction of proteasome cleavages
    - Prediction of proteasome cleavage sites (see Resources)
- Virus epitopes
- Allergens
  - AllALLERGY
  - Allergome - A platform for allergen knowledge (needs registration)
  - Allergy and Immunology - Hardin MD
  - Les bases de données d'allergènes (diaporama), Marie-Paule Lefranc, Montpellier, France
  - Food vegetal allergens, IMGT Lexique, LIGM, Montpellier, France.
  - Food animal allergens, IMGT Lexique, LIGM, Montpellier, France.
  - Cross-reactivities between allergens, IMGT Lexique, LIGM, Montpellier, France.
  - Gliadins, lectins and profilins from wheat (Triticum aestivum, T. wartu, T. durum), IMGT Lexique, LIGM, Montpellier, France.
Immunoglobulin superfamily (IgSF)
- IgSF chains and V-LIKE-DOMAIN. IMGT unique numbering for immunoglobulin and T cell receptor variable domains and Ig superfamily V-like domains. Lefranc, M.-P. et al., Dev. Comp. Immunol., 27, 55-77 (2003) PMID: 12477501 with permission from Elsevier
- IgSF chains and C-LIKE-DOMAIN. IMGT unique numbering for immunoglobulin and T cell receptor constant domains and Ig superfamily C-like domains. Lefranc, M.-P. et al., Dev. Comp. Immunol., 29, 185-203 (2005) PMID: 15572068 with permission from Elsevier
- IMGT Repertoire (RPI) 2. Proteins and alleles
- IMGT Repertoire (RPI) 4. IgSF other than IG or TR
Major histocompatibily complex superfamily (MhcSF)
- IMGT Repertoire 2. Proteins and alleles (RPI)
- IMGT Repertoire - MhcSF other than MHC
- MhcSF chains and G-LIKE-DOMAIN. IMGT unique numbering for MHC groove G-DOMAIN and MHC superfamily (MhcSF) G-LIKE-DOMAIN. Lefranc, M.-P. et al., Dev. Comp. Immunol., 29, 917-938 (2005) PMID: 15936075 with permission from Elsevier
Protein expression
- Human Protein Atlas
Peptides
- The Peptide Resource Page
Adhesion molecules
Killer cell immunoglobulin-like receptors (KIR)
- dbLRC, NCBI, USA
- KIR family (PROW)
- NK receptors / Récepteurs des cellules NK, IMGT Education, LIGM, Montpellier, France.
- Nomenclature of the human LRC (Leucocyte Receptor Complex) genes: LILR/ILT nd KIR (19q13.42), IMGT Education, LIGM, Montpellier, France.
- The KIR Gene Cluster, Mary Carrington and Paul Norman, Bethesda (MD), National Library of Medicine (US), NCBI, 2003
Immunodeficiency
- ImmunoDeficiency Resource (IDR), University of Tampere, Finland
Integrins
- Integrins
- Diversity of integrins (IMGT Education)
Translocations
- Atlas of Genetics and Cytogenetics in Oncology and Haematology
Tumour cells
- ESTDAB - European Searchable Tumour Line Database, allows search of tumour cell lines, predominantly melanoma, by parameters such as HLA genotype, tumour antigens, etc.
Pathogens
- Pathogen invertebrate vectors
  - VectorBase, a web resource for invertebrate vectors of human pathogens. Currently contains genome information for Anopheles gambiae, a vector for the Plasmodium protozoan agent causing malaria, and Aedes aegypti, a vector for the flaviviral agents causing Yellow fever and Dengue fever.
- Pathogen-host interactions
  - PHIDIAS, a Pathogen-Host Interaction Data Integration and Analysis System.

Nobel lectures

Antibody structure and molecular immunology. Nobel Lecture, 12 December 1972. Gerald Edelman
The role of MHC gene products in immune regulation and its relevance to alloreactivity. Nobel lecture, 8 December 1980. Baruj Benacerraf
The major histocompatibility complex in man - Past, present, and future concepts. Nobel lecture, 8 December 1980. Jean Dausset
Studies in histocompatibility. Nobel lecture, 8 December 1980. George D. Snell
From the structure of antibodies to the diversification of the immune response. Nobel Lecture, 8 December 1984. César Milstein

Documentation

'History of MHC-HLA' references (including some early reviews and citation classics) M.Tevfik Dorak
IMGT bioinformatic tools for immunoglobulin and T cell receptor sequence analysis, Marie-Paule Lefranc, Bioinformatics from a User's Perspective
Report on the Novartis foundation Symposium 254, 'Immunoinformatics: bioinformatics strategies for better understanding of immune function' London, 8-10 october 2002. Novartis Foundation Bulletin 16 with the authorization of the Novartis Foundation

IMGT posters and diaporama

Meeting announcements

Networks

ESF European Science Foundation - Network on Myelin Structure and its Role in Autoimmunity

IMGT Web resources