HIV Molecular Immunology Database: Tools & Links

Tools Produced by the Los Alamos HIV Databases

• QuickAlign Align amino acids or nucleotides against our alignments
• PeptGen Generate overlapping peptides for any protein
• PepMap Generate peptide maps in Fasta, HTML and PDF formats
• Hepitope Search for hopeful epitopes based on HLA enrichment
• HLA Frequency Analysis Tools Calculate HLA frequencies or HLA linkage disequilibrium in a population
• ELF Epitope location finder
• Motif Scan Scan alignments for HLA binding motifs
  • HLA genotype/serotype dictionary
  • HLA genotype/motif dictionary
  • HLA supertype dictionaries
• HIV/SIV Sequence Locator Tool Formerly the HXB2 Numbering Engine
• SeqPublish Produce pretty alignments for publication
• BLAST Search sequences against our annotated HIV sequences
• Heatmap Display a table of numbers using colors to represent the numerical values
• Mosaic Vaccine Tool Suite Design and assess polyvalent protein sequences for T-cell vaccines
• N-Glycosite Find N-linked glycosylation sites
• Highlighter Highlight matches and mismatches in a set of aligned sequences

• All Tools List of all software and tools in both the HIV sequence and immunology databases

External Tools for Epitope Prediction

• BIMAS HLA Peptide Binding Predictions Ranks potential n-mer peptides based on a predicted half-time of dissociation to HLA class I molecules
• SYFPEITHI Epitope Prediction Predicts the binding of a given amino acid sequence to a defined HLA type
• PAProC Predicts cleavages by human and yeast 20S proteasomes
• PREDEP MHC class I epitope prediction
• MHCPred Predicts MHC/peptide or TAP/peptide IC₅₀ binding values
• Microsoft Research Epitope Predictor Computes the probability that a given n-mer is a T-cell epitope restricted to a given HLA allele
• Max Planck Institute
  • FRAGPredict Prediction of proteasome cleavage
  • MAPPP Prediction of MHC-I antigenic peptide processing
• Immune Epitope Database (IEDB)
  • MHC Class I Binding
  • MHC Class II Binding
  • NetChop and NetCTL Predictors of proteasomal processing and T cell epitopes
  • MHC Processing Predictions Combines predictors of proteasomal processing, TAP transport, and MHC binding to produce an overall score for each peptide's intrinsic potential of being a T-cell epitope
• Center for Biological Sequence Analysis (CBS)
  • NetMHC Predicts MHC binding ability of peptides
  • NetMHCpan Predictions of peptide binding to any HLA-A and -B locus protein of known sequence
  • NetChop Predicts cleavage sites of the human proteasome
  • NetCTL Predicts CTL epitopes by combining MHC supertype binding, TAP binding, and proteasome cleavage scores
  • HLArestrictor Given a peptide sequence and the HLA type of an individual, predicts all 8-11mer peptide binders and minimal epitopes
• IMTech
  • CTLPred Prediction of CTL epitopes, combining MHC binding, TAP binding, and cleavage
  • MHC2Pred Prediction of promiscuous MHC class II binders
  • MMBPred Prediction of promiscuous MHC class I binders and mutations that allow high-affinity binding
  • Pcleavage Predicted proteasome or immunoproteasome cleavage
  • ProPred Predicted MHC class II-peptide binding
  • ProPred-I Predicted MHC class I-peptide binding; optional proteasome cleavage filter
  • TAPPred Prediction of binding affinity of TAP proteins
  • MHCBN 4.0 MHC-peptide binders and nonbinders, TAP-peptide binders and nonbinders, and T-cell epitopes

External Immunology Databases

• The SYFPEITHI Database MHC ligands, peptide motifs and epitope prediction
• Immune Epitope Database (IEDB) Databases of HIV and HCV epitopes
• dbMHC MHC database at NCBI
• HLA Nomenclature home page
• Nomenclature for Factors of the HLA System Update to HLA Nomenclature, 2009
• The IMGT/HLA Dictionary at EBI
• International Immunogenetics Database (IMGT) Aligned and annotated HLA sequences
• EMBL-IMGT HLA Allele Query Form Aligned and annotated T-cell receptor sequences nomenclature
• MHC Haplotype Project Haplotypes of MHC-linked diseases, with complete genomic sequences, variations (SNPs and DIPs), and ancestral relationships
• Jenner Institute
  • JenPep Peptide binding database
  • AntiJen Binding data for MHC-ligand interactions, TCR-MHC complexes, and TAP
• HCV Immunology Database HCV epitopes
• RCSB Protein Data Bank (PDB) Structural database and viewing tools, MHC/peptide/TCR combinations

HIV Vaccine Studies and Related Databases

• IAVI Database of Preventive AIDS Vaccines in Human Trials
• Database of HIV Vaccines in Development from The Pipeline Project
• NIH AIDSinfo HIV/AIDS Vaccines
• LANL HIV/SIV Vaccine Trials Database

Other Immunology Links

• NIH AIDS Research and Reference Program HIV immunology reagents
• Antibody Resource
• Immunology Link site
• NIBSC, Centralised Facility for AIDS Reagents
• HLA Informatics Group-Anthony Nolan Bone Marrow Trust
• Molecular Immunology Foundation
• Allele Project Allele frequencies in worldwide populations
• Immunopaedia A site designed to help close the gap between clinical observations and immunology knowledge

HIV/AIDS Links

• HIV/AIDS Links List of many HIV/AIDS-related links maintained by the HIV Sequence Database