Bioinformatics-Epitopes and MHC/HLA Resources

Analytical and Computational Tools

• HIV Databases
  
  • ELF/Epitope Location Finder
    Search a submitted protein sequence for known epitopes from our immunology databases; epitopes predicted by consensus binding motifs; and epitopes predicted by the IEDB binding algorithm.
  • Hepitope/HLA-Enriched Possible Epitope
    The Hepitope tool searches for hopeful-epitopes or "Hepitopes."
  • HLA Analysis Tools
    These tools calculate and graph HLA frequencies in a population; search for HLA linkage disequilibrium in a population; and compare the HLA frequencies in two populations.
  • Human Immunology Project Consortium
    The HIPC capitalizes on recent advances in immune profiling methods to create a novel public resource that characterizes diverse states of the human immune system following infection; prior to and following vaccination against an infectious disease; or prior to and following treatment with an immune adjuvant that targets a known innate immune receptor(s).
  • Mosaic Vaccine Tool Suite
    The three tools that make up this suite allow users to design and assess vaccine candidate protein sequences.
  • Motif Scan/HIV HLA Anchor Residue Motifs
    This page serves three functions: 1) find HLA anchor residue motifs within protein sequences for specified HLA genotypes, serotypes, or supertypes; 2) search any single protein for all known HLA anchor residue motifs; and 3) view motif libraries.
  • PepMap
    The PepMap tool maps an input set of peptides on the HIV reference sequence HXB2.
• Immune Epitope Database and Analysis Resource (IEDB)
  
  • B Cell Epitope Prediction Tools
    These tools predict IC50 values for peptides binding to specific MHC molecules.
  • T Cell Epitope Prediction Tools
    These tools predict IC50 values for peptides binding to specific MHC molecules.
  • Epitope Cluster Analysis
    This tool groups epitopes into clusters based on sequence identity.
  • Epitope Conversancy Analysis
    This tool computes the degree of conservancy of an epitope within a given protein sequence set at a given identity level.
  • Epitope Sequence and 3D Structural Homology Mapping
    A tool for immunologists to study the three dimensional structural features of an epitope sequence and its source sequence.
  • Population Coverage Calculation
    The tools are intended for the detailed analysis of a known epitope sequence or group of sequences.
• MHC Sequence Feature Variant Type (SFVT) Analysis
  This analysis enables genetic association analysis of classical HLA protein sub-regions defined with structural (e.g., helix) and functional (e.g., binding site) information.

Databases and Data Sets

• HIV Database
  
  • Antibody Database
    HIV molecular immunology database
  • CTL/CD8+ T-Cell Epitope Database
    HIV molecular immunology database
  • Epitope Alignments
    The alignments are FASTA files of the unique epitope sequences aligned to the LANL HIV subtype reference alignments.
  • Epitope Tables
    These tables summarize the epitopes from the database.
  • HLA Analysis Tools
    These tool calculate and graph HLA frequencies in a population; search for HLA linkage disequilibrium in a population; and compare the HLA frequencies in two populations
  • HLA Typing and Epitope Mapping
    These data tables describe: peptides; subjects (e.g., each person's HLA and reactive peptides); and maps of overlapping peptides and HLA types of responding individuals.
  • Motif Scan/HIV HLA Anchor Residue Motifs
    This page serves three functions: 1) find HLA anchor residue motifs within protein sequences for specified HLA genotypes, serotypes, or supertypes; 2) search any single protein for all known HLA anchor residue motifs, and 3) view motif libraries.
  • SVG Epitope Maps
    These maps are implemented with SVG (scalable vector graphics), which is supported by most, but not all, major web browsers.
  • T Helper/CD4+ T-Cell Epitope Database
    The HIV databases contain data on HIV genetic sequences, immunological epitopes, drug resistance-associated mutations, and vaccine trials.
• Immune Epitope Database and Analysis Resource (IEDB)
  The IEDB contains data related to antibody and T cell epitopes for humans, non-human primates, rodents, and other animal species.
  • B Cell Search
  • Epitope Search
  • Identifier Search
  • MHC Ligand Elution Search
  • T Cell Search
• MHC Allele Search
  Complete DNA and protein sequences, sequence features, and population frequencies of MHC alleles.
• Immune Epitope Search
  Search for experimentally determined and predicted epitopes.
• ViPR Search
  The Virus Pathogen Resource is a useful resource for the virology research community designed to assist users with various projects involving sequence and structure analysis, comparative genomics, and virus phenotype studies among others.

Visualization and Modeling Tools

• HLA Analysis Tools
  These tools calculate and graph HLA frequencies in a population; search for HLA linkage disequilibrium in a population; and compare the HLA frequencies in two populations
• Immunology Database and Analysis Portal (ImmPORT)
  
  • Jmol MHC Sequencing Feature Structure Viewer
  • IMHC Allele Search
• Protein Feature Accent
  View 3D structures of HIV proteins and map a desired sequence (e.g., short functional domain or epitope) directly onto the interactive graphic.

Contact Information

For more information on Bioinformatics-Epitopes and MHC/HLA Resources, email:
Bioinformatics and Computational Sciences Branch