HIV molecular immunology database
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Tools
All Immunology Tools
Quickalign
PeptGen
Motif Scan
Sequence Locator
ELF
Hepitope
HLA Freq Analysis
Mosaic
Epicover
Posicover
PepMap
Heatmap
N-Glycosite
Highlighter
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Epitope Alignments
Epitope Variants
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Sequence Alignments
Tutorials
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 IC
50
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
Questions or comments? Contact us at
immuno@lanl.gov