Some useful links on immunoinformatics

Some useful links on immunoinformatics :

Minimal Information about T Cell Assays (MIATA) project 

IMGT/HLA Database at European Bioinformatics Institute (EBI) contains the official sequences of the WHO Nomenclature Committee for Factors of the HLA System

dbMinor at Leiden University : the minor Histocompatibility Knowledge Database

AntigenDB (mirror) : 500 antigens from 44 important pathogenic species, including epitope search

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)
• 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 : gene frequency data on human populations supported by the U. S. National Science Foundation.

HLAMatchmaker by Rene' Duquesnoy : eplet mismatching calculators

MHC-binding epitope predictions :

• on payment immunogenicity screening :
• EpiVax, Inc. (on payment)
• Epibase^® by Lonza.
• Prediction Algorithm for Proteosomal Cleavages (PAProC)
• SYFPEITHI : epitope prediction by BioMedical Informatics (BMI) - Heidelberg (after the name of first natural MHC ligand directly msequenced, the nonapeptide SYFPEITHI eluted from H-2 K^d molecules of a mouse tumour line, P815, ortholog of human JAK1)
• Immune Epitope Database (IEDB) contains data related to antibody, T cell epitopes, and MHC binding data for humans, non-human primates, rodents, and other animal species
• NetMHCpan 2.4 server : database for quantitative predictions of peptide binding to any HLA-A and -B protein sequence.
• MHCPred 2.0
• RANKPEP at Harvard University
• Institute for Transfusion Medicine, Hannover Medical School, Germany :
• HistoCheck^ref (free registration required)
• PeptideCheck (free registration required)
• HaploCheck (free registration required)
• MHCO : An Ontology for Major Histocompatibility Complex Alleles and Molecules
• class I MHC-binding prediction :
• HLA-peptide binding prediction (human and murine) at BioInformatics & Molecular Analysis Section (BIMAS)
• 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)^ref.
• NetMHC^{ref1, ref2, ref3}
• ProPred-I : the promiscuous human and murine MHC class-I binding peptide prediction server
• MAPPP  at Max-Planck-Institute for Infection  Biology : human and murine MHC-I binding prediction  using BIMAS or SYFPEITHI matrices
• class II MHC-binding prediction :
• EpiPredict
• MHC-Thread
• ProPred^ref
• Vaccinome's TEPITOPE

Print this post