HIV molecular immunology database
The HIV immunology database is a repository of information about HIV epitopes and antibody binding sites, plus associated tools. For more information, see About the Immunology Database.
The database staff includes immunologists, molecular biologists, sequence analysts, computer technicians, post-docs, and graduate research assistants. We are part of the Theoretical Biology and Biophysics Group (T-6) at the Los Alamos National Laboratory. We are funded by the Division of AIDS of the National Institute of Allergy and Infectious Diseases through an interagency agreement with the Department of Energy. We are advised by a group of external database editors.
Our databases are organized around several areas of virus research. The links on the menu will take you to the other areas of this site. In particular, this immunology database is closely tied to the HIV Sequence Database.
The information on this site assists researchers who study the AIDS virus and are seeking ways of defeating it. The information available here is not directly helpful to patients. We are not qualified to give medical advice of any kind. You can find links to websites with information about AIDS in the HIV Sequence Database Links.
Most tools provide a Help file with information about the data type(s) accepted. In general, data and sequences should be in appropriate text file formats, not in Word (.doc) or other word processing formats. Sequences are accepted in a variety of common formats. If you need help, contact us.
Yes, we can help troubleshoot the problem, and your problem may help us improve our tools. Please write to firstname.lastname@example.org; include your input file(s) if possible.
Yes, but be careful. Names like RY11 are not specific - there may be multiple RY11's. Furthermore, the results will not include every entry for RY11, as some authors don't use these names. We recommend searching for the common name only as a way to find the full epitope sequence (or its coordinates), and then using this information to do the search.
The "A list" is a nickname for the "Best-defined" epitopes. The list of Best-defined epitopes is revised yearly by Christian Brander and colleagues. This list includes only those HIV-1 epitopes that are optimal and well-substantiated.
In contrast, the CTL "B list" is the summary table of all CTL epitopes in our database.
Not all epitopes from a specific map location share exactly the same amino acid sequence. The sequence shown on the map is the B-clade reference sequence HXB2; the epitopes shown may have come from another strain of HIV and thus have a different sequence. The next question addresses how to obtain details for all epitopes that appear on the map.
The maps and tables are based on exactly the same data. They contain the vast majority of the data currently available through the search interface. There may a few newly-entered epitopes available through the search interface that are not yet in the maps and tables.
We provide a search interface and table of Epitope Variants and Escape Mutations.
The focus of this database is HIV-1. Some HIV-2 epitopes are included in our searches, maps and tables. SIV epitope data are not incorporated into our searchable databases. We provide a table of SIV epitopes, based on a 2006 review article (PDF): Beyond Mamu-A*01+ Indian Rhesus Macaques: Continued Discovery of New MHC Class I Molecules that Bind Epitopes from the Simian AIDS Viruses, by Loffredo et al. 2006.
We also provide:
The antibody database is structured differently. While the CTL and helper databases have a separate database entry for each reference, the antibody database has a single entry for each antibody, often with many references.
You can limit the number of notes by including an author name, keyword, or note text, and selecting the option to show only the notes related to your selection.
Some of our older database entries include contact information for the person who originally described the antibody. Searching for the antibody name and the keyword "antibody generation" should lead to the note for the original reference. You can also try a web search engine to find commercial or other sources.
HXB2 is a subtype B HIV-1 isolate used in all our databases as the reference strain for aligning and numbering HIV-1 sequences. The actual sequence (either DNA or protein) can be obtained from any of our premade HIV-1 Alignments, Sequence Locator tool, or from the Sequence Search Interface.
Just put your epitope sequence into Sequence Locator.
In the sequence database, we have informational web pages that describe the subtypes (clades) of HIV. Subtypes are usually indicated by a letter (A, B, C, etc.). HIV also has circulating recombinant forms (CRFs), which are recombinants of two or more subtypes. For more information, see Overview of Subtypes and HIV Nomenclature.
From the CTL, Helper, or Antibody search results, click the link marked "Epitope Alignment" to see that specific epitope aligned to a large set of sequences from the sequence database. In addition, we provide premade Epitope Alignments, which show all epitopes aligned to subtype reference sequences. The QuickAlign tool provides additional options.
HIV-1 p15 is a domain within the heterodimeric reverse transcriptase (RT) enzyme. It is included as part of RT.
Members of our staff review published articles and enter the information manually. We strive for accuracy, and we have several quality assurance mechanisms. Nonetheless, we are human, and occasional errors occur. Before using the information presented here, confirm it by reading the original reference(s).
New data are entered into the searchable databases almost daily. New data are entered into the maps and tables approximately weekly. The current database statistics (total numbers of database entries) are shown on the About the Immunology Database page; these statistics are updated daily.
Keywords are chosen as each published paper is entered. The keywords are used by our database in ways that we have found useful, not necessary as used by the authors of the paper. If you have any questions about how we use particular keywords, please contact us.
In general, we enter the HLA as it is provided in the original publication.
Yes! Please write to email@example.com. We will be happy to look into it and correct it if necessary.
We provide such a database as part of the Motifscan tool. The data are presented as tables in both the Binding Motif Dictionary and Supertype Dictionary. Binding motif information is also provided by the ELF tool, along with binding predictions.
We currently have several large sets of this type of data that you can search. See HLATEM.
The HIV Sequence Database contains many sequences from patients of known HLA types. Using the Sequence Search Interface, click on "Patient Information" and check the box labeled "Only sequences with HLA information". Sequences may be downloaded as DNA or as protein(s).
Yes, please write to firstname.lastname@example.org. If you do not receive an answer within 3 business days, please write again. We try to answer every inquiry promptly, but occasionally one is missed. For questions related to the LANL Sequence Database, see HIV Sequence Database FAQ.