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 
(LIGM, Université
Montpellier 2, CNRS, Montpellier, France)
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
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
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
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)
- DBAASP - Database of Antimicrobial Activity and Structure of Peptides
- 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
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
- Analysis of the V-J and V-D-J junction
- Gene identification
- Phylogeny
- Sequence comparison
- 3D Structures
- Modelisation
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
- Gene identification
- Phylogeny
- Sequence comparison
- 3D Structures
Major histocompatibility complex (MHC)
- Sequence comparison
- 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.
Recombination signal (RS)
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
- IHWG International
Histocompatibility Working Group
- The Molecular
Immunology Foundation
- WMDA World Marrow
Donor Association
Genomes
Antigens
Antigens eliciting an antibody response
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
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)
Major histocompatibily complex superfamily
(MhcSF)
Protein expression
Peptides
Killer cell immunoglobulin-like receptors (KIR)
- Chromosome
19 LRC Haplotype Project
- dbLRC,
NCBI, USA
- 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
Integrins
Translocations
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.
Blogs
Documentation
- 'History
of MHC-HLA' references (including some early reviews and citation
classics) M. Tevfik Dorak
- Report on the Novartis foundation Symposium 254,
'Immunoinformatics: bioinformatics strategies for better
understanding of immune function' London, 8-10 october 2002. Novartis foundation
Networks
Nobel lectures
- Created:
- 14/11/2002
- Last updated:
-
Friday, 22-Mar-2013 22:05:44 CET
- Editors:
- Valérie Thouvenin-Contet, Ruth Henry, Chantal
Ginestoux
