Monday, December 12, 2011

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 :

  • 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 Kd 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 :
      • HistoCheckref (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 databaseref
      • LpPep (for HLA-A2)ref.
      • NetMHCref1, 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 :
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