HIV molecular immunology database
The HIV Molecular Immunology Database is an annotated, searchable collection of HIV-1 cytotoxic and helper T-cell epitopes and antibody binding sites. The goal of this database is to provide a comprehensive listing of defined HIV epitopes. These data are also printed in the HIV Molecular Immunology compendium, which is updated yearly and provided free of charge to scientific researchers, both by online download and as a printed copy. Compendium editors: Bette Korber, Christian Brander, Barton F. Haynes, Richard Koup, John P. Moore, Bruce D. Walker, and David I. Watkins. Publisher: Los Alamos National Laboratory: Theoretical Biology and Biophysics, Los Alamos, New Mexico.
The publication of the HIV Molecular Immunology Compendium is funded by the Division of AIDS, National Institute of Allergy and Infectious Diseases, through an interagency agreement with the U.S. Department of Energy. The project officer is Geetha Bansal.
HIV Molecular Immunology is a companion volume to Human Retroviruses and AIDS Genetic Sequence Compendium. This publication is the printed version of this website. The web interface for this relational database has many search options, as well as interactive tools to help immunologists design reagents and interpret their results. For information about referencing this database in publications, please see How to Cite the HIV Immunology Database.
The data included in this database are extracted from the HIV immunology literature. HIV-specific B-cell and T-cell responses are summarized and annotated. Immunological responses are divided into three sections, CTL (CD8+), T helper (CD4+), and antibody. Within these sections, defined epitopes are organized by protein and binding sites within each protein, moving from left to right through the coding regions spanning the HIV genome. We include human responses to natural HIV infections, as well as vaccine studies in a range of animal models and human trials. Responses that are not specifically defined, such as responses to whole proteins or monoclonal antibody responses to discontinuous epitopes, are summarized at the end of each protein sub-section. Studies describing general HIV responses to the virus, but not to any specific protein, are included at the end of each section.
The annotation includes information such as cross-reactivity, escape mutations, antibody sequence, TCR usage, functional domains that overlap with an epitope, immune response associations with rates of progression and therapy, and how specific epitopes were experimentally defined. Basic information such as HLA specificities for T-cell epitopes, isotypes of monoclonal antibodies, and epitope sequences are included whenever possible. All studies that we can find that incorporate the use of a specific monoclonal antibody are included in the entry for that antibody. A single T-cell epitope can have multiple entries, generally one entry per study.
Finally, tables and maps of all defined linear epitopes relative to the HXB2 reference proteins are provided. Alignments of CTL, helper T-cell, and antibody epitopes are available through the search interfaces.
Only responses to HIV-1 and HIV-2 are included in the database. CTL responses to SIVs have been periodically summarized in our review section by Dr. Dave Watkins and colleagues. (For their most recent review, please see: Where Have All The Monkeys Gone?: Evaluating SIV-Specific CTL in the Post-Mamu-A*01 Era, David H. O'Connor, Todd M. Allen, and David I. Watkins, in the 2001 HIV Immunology compendium). Dr. Christian Brander and colleagues annually provide a concise listing of the best-defined CTL epitopes. Additional reviews that our editorial board deems of general interest to the HIV research immunology community are solicited each year. This year's reviews are printed in the first section of this database and on-line in review articles.
Comments on the database are always welcome, and can be sent via e-mail to immuno@lanl.gov.
HIV Immunology database record counts as of 13 January 2009, 18:31 MST.
| Database | Records | References |
|---|---|---|
| CTL, CD8+ | 4953 | 905 |
| T-helper, CD4+ | 1023 | 311 |
| Antibodies | 1448 | 1026 |
| Total bibliography | 2116 | |
The "total bibliography" count is less than the sum of the "references" column because some references appear in more than one section of the database.
Last modified: Tue Dec 6 08:59:13 MST 2005