The purpose of the database is to serve as a central interactive interface for viewing an ensemble of the known interactions between individual HIV-1 proteins and human proteins. The HIV-1, Human Protein Interaction Database home page (http://www.ncbi.nlm.nih.gov/RefSeq/HIVInteractions/
) enables users to simultaneously view and download a variety of reports detailing interactions for each HIV-1 protein. The database is structured by initial searches for the nine HIV proteins (e.g. Gag, Pol, Env, Tat, Rev, Nef, Vif, Vpr and Vpu), listed in the top right panel of the home page. An alphabetical report of all interacting human proteins is accessed by following the link for any of the HIV-1 proteins. The HIV-1 proteins can also be searched based on their components, for example HIV-1 Envelope can be searched either for the entire protein gp160, or separately for the gp120 surface glycoprotein or the gp41 transmembrane protein, which result from proteolytic cleavage of gp160. The HIV-to-human protein interactions are categorized by 43 interaction keywords (e.g. activates, associates with, binds, cleaves, complexes with, deglycosylates, inhibits, modulates, upregulates
, etc.). A query interface allows for searching of the database to identify cellular proteins that have a specific type of interaction with a viral protein based on these keywords. The report can be customized to categories of interest by selecting a specific HIV protein and interaction keywords from the drop down menus. Reports can be viewed as a web page, or downloaded as a text file for later use. In addition, to help facilitate the retrieval of related data, links to other database resources, such as the Database of Interacting Proteins (DIP; 3
), the Molecular INTeraction Database (MINT; 4
), the Binding Database (5
) and the Los Alamos National Laboratories (LANL) HIV Databases (6
), are provided on the home page.
depicts the report and search interface page for the HIV-1 Gag polyprotein and its cleavage products. As mentioned earlier, the drop down menus (A) allow for the selection of data related to the individual Gag cleavage products (e.g. matrix, capsid, nucleocapsid, p1 and p6) and also facilitate searching by specific keywords (e.g. associates with, binds and inhibits) that represent the relationship between the viral proteins and the interacting human proteins (B). Reports can either be viewed online or downloaded in ASCII format and contain the HIV-1 Tax ID, HIV-1 Gene ID, HIV-1 protein accession number, HIV-1 protein name, the Interaction Keyword, the human Tax ID, human Gene ID, human protein accession number, human protein name, the PMID(s), the modification date and the interaction description.
Figure 1. Partial report page of HIV-1 Gag interactions with human proteins. (A) All or part of the interaction data available for an HIV-1 protein can be accessed using the drop down menus. (B) The interacting relationship between HIV-1 and human proteins is reported (more ...)