Softwares :

• IMGT/HLA Database at EBI, Anthony Nolan Research Institute contains the official sequences of the WHO Nomenclature Committee for Factors of the HLA System
• dbMinor at Leiden University
• AntigenDB (mirror) : 500 antigens from 44 important pathogenic species
• Polymorphisms
• Immuno Polymorphism Database (IPD) at EBI :
• KIR
• KIR ligand calculator (search for mismatches between KIR ligands)
• MHC (nomenclature in cattle, canines, felines, fish, non-human primates, rats, sheep, and swine)
• human platelet antigens (HPA)
• European Searchable Tumour cell Line Database (ESTDAB)
• MaHCO Ontology (mirror)
• MHC motif viewer : display of the likely binding motif for all human class I proteins of the loci HLA A, B, C, and E and for MHC class I molecules from chimpanzee (Pan troglodytes), rhesus monkey (Macaca mulatta), and mouse (Mus musculus).
• Allele*Frequencies.net in Worldwide population
• ALlele FREquency Database (ALFRED) at Yale University
• HLAMatchmaker
• MHC-binding epitope prediction
• PREDICT : prediction of MHC (HLA-DRB1*0401) binding peptides using artificial neural network (ANN), motifs, and Hidden Markov's Model by V.Brusic, Judice L.Y.Koh, Zhang GuangLan and T.Kandasamy
• EpiMatrix by EpiVax, Inc. (on payment)
• HLA peptide binding prediction (human and murine) at BioInformatics & Molecular Analysis Section (BIMAS)
• SYFPEITHI : epitope prediction by BioMedical Informatics (BMI) - Heidelberg contains a collection of MHC class I and class II ligands and peptide motifs of humans and other species accessible as individual entries. Searches for MHC alleles, MHC motifs, natural ligands, T-cell epitopes, source proteins/organisms and references are possible. Hyperlinks to the EMBL and PubMed databases are included. In addition, ligand predictions are available for a number of MHC allelic products. The database content is restricted to published data only^ref. The first natural MHC ligand to be sequenced directly was the nonapeptide SYFPEITHI eluted from H-2 K^d molecules of a mouse tumour line, P815. A GenBank search indicated high homology to a nonapeptide contained within the human tyrosine kinase JAK1: SFFPEITHI, residues 355-363. So SYFPEITHI is a dominant H2-K^d ligand derived from the JAK1 tyrosine kinase^{ref1, ref2}
• Epibase^® can be applied to generate:
• T-Helper epitope profiles: assessment of the immunogenicity of therapeutic proteins (such as antibodies, proteases, etc.) as a function of HLA Class II haplotype.
• CTL epitope profiles: assessment of the epitope content and HLA binding spectrum for viral or bacterial antigens or for cancer associated antigens. The major aim is to define proteins or parts derived thereof for subsequent vaccine lead development.
• CTL poly-epitope vaccine leads: identification of a set of strong epitopes to make a vaccine that shows efficacy across different HLA types.
• Immunotuning^®: the identification of T-Helper epitopes in therapeutic proteins and the subsequent removal of these epitopes through amino acid substitutions that do not alter the stability or the activity of the molecule. The required substitutions are identified using AlgoNomics’ Tripole^® platform.
• Epitope Identification System (EIS) by Epimmune
• Immune Epitope Database (IEDB) 2.0 contains data related to antibody and T cell epitopes for humans, non-human primates, rodents, and other animal species. The database also contains MHC binding data from a variety of different antigenic sources and immune epitope data from the FIMM (Brusic), HLA Ligand (Hildebrand), TopBank (Sette), and MHC binding (Buus) databases^ref
• NetMHCpan :database for quantitative predictions of peptide binding to any HLA-A and -B protein sequence. Uses Artificial Neural Networks to predict peptide binding based on sequence of any HLA protein sequence
• MHCPred : predicting the binding affinity for human MHC I and II molecules using additive methods
• RANKPEP : prediction of binding peptides to human and murine class I and II MHC molecules at the Molecular Immunology Foundation
• Institute for Transfusion Medicine, Hannover Medical School, Germany :
• HistoCheck^ref
• PeptideCheck
• HaploCheck
• StemNet
• GvL peptide prediction
• class I MHC-binding prediction :
• SVMHC uses support vector machines and currently contains prediction for 26 MHC class I types from the MHCPEP database or alternatively 6 MHC class I types from the higher quality SYFPEITHI database^ref
• LpPep (for HLA-A2) : various methods have been proposed to predict the binding affinities of peptides to MHC-I molecules based on experimental binding data. They can be classified into 2 groups:
• AIB methods that assume independent contributions of all peptide positions to the binding to MHC-I molecule (e.g. scoring matrices)
• general methods which can take into account interactions between different positions (e.g. artificial neural networks).
The best AIB methods gave significantly better predictions than three previously published general methods, possibly due to the lack of a sufficient training data for the general methods. The best results, however, were achieved with our newly developed general method, which combined a matrix describing independent binding with pair coefficients describing pair-wise interactions between peptide positions. The pair coefficients consistently but only slightly improved prediction accuracy, and were much smaller than the matrix entries. This explains why neglecting them-as is done in AIB methods-can still lead to good predictions^ref.
• NetMHC 2.0 server predicts binding of peptides to a number of different HLA alleles using artificial neural networks (ANNs) and hidden markov models (HMMs). Predictions can be obtained for 12 supertypes, and 120 individual alleles using matrices (ungapped HMMs) generated with data from public databases. Furthermore ANNs have been trained for 10 different alleles representing 7 supertypes^{ref1, ref2, ref3}
• ProPred-I : the promiscuous human and murine MHC class-I binding peptide prediction server
• MAPPP : human and murine MHC-I binding prediction at Max-Planck-Institute for Infection Biology using BIMAS or SYFPEITHI matrices
• class II MHC-binding prediction :
• EpiPredict : HLA class II-restricted T cell epitopes and ligands
• MHC-Thread: HLA class II predictions
• ProPred: MHC class II binding peptide prediction server^ref
• Vaccinome's TEPITOPE is a software package for the prediction of promiscuous HLA-class II binding peptides and human T-cell epitopes.
• The value of predictive algorithms for identifying CD8⁺ T (T_CD8+)-cell epitopes has not been adequately tested experimentally. Conventional bioinformatic methods predict the vast majority of T_CD8+-cell epitopes derived from vaccinia virus WR strain (VACV-WR) in the H-2^b mouse model. This approach reveals the breadth of T-cell responses to vaccinia, a widely studied murine viral infection model, and may provide a tool for developing comprehensive antigenic maps of any complex pathogen^ref

• The IMGT Immunoinformatics page
• University of Tuebingen
• Ecole Politechnique Federale de Lausanne
• RIKEN Institute
• Edward Jenner Institute for Vaccine Research
• Université Montpellier II
• Birkbeck College

• Workshop on Artificial Immune Systems and Immune System Modelling 4th April 2006; part of AISB'06: Adaptation in Artificial and Biological Systems, University of Bristol, Bristol, England
• 5th International Conference on Artificial Immune Systems (ICARIS), 4th-6th September, 2006 in Instituto Gulbenkian de Ciência, Oeiras, Portugal (see 4th conference)
• 13th Signal and Signal Processing in the Immune System EFIS Conference, Balatonöszöd, Hungary, September 7-11, 2005