Because the curation of PPIs from literature can be variable, it is highly recommended that users consult the primary literature to verify information about PPIs of interest.
I. HELP WITH THE VIEWER
Q1. I'm having trouble getting the Navigator viewer to work. What should I do?
Q1. Where does confidence score come from? Is it supplied by the databases?
A1. Human interactions are displayed using the score calculated within the HIPPIE database.  A crude confidence score is calculated in GPS-Prot for HIV-1 interactions as described here.
Q2. Why doesn't the search work when I enter yeast genes?
A2. GPS-Prot is implemented only for human and HIV proteins at this time.
Q3. What does it mean when I get the message NO RESULTS FOR QUERY?
A3. A mismatch between gene name and organism (e.g. you've entered an HIV gene with the organism set to human).
Or you have selected only genetic/proteomic profiling datasets, which do not contain PPI information.
Or you have used a Gene Name that is invalid. Try using the standard gene name rather than a synonym or familiar name.
Or you have used an invalid UniProt ID.
Or you have not selected databases that contain interactions with your query protein. FOR HIV PROTEINS, YOU MUST SELECT AT LEAST ONE OF: HARC Proteomics or HHPID databases, which contain HIV-host interactions.
III. NAVIGATOR WINDOW
Q1. What's the difference between "PPI" and "PPI + Screen Hit" (green and yellow nodes, respectively, in Navigator)?
A1. PPI (green nodes) refers to an experimentally determined protein-protein interaction (e.g. in MINT, DIP, HPRD or other PPI database). This is the data used to build the networks. Screen Hit refers to proteins identified in various genetic or proteomic screens for HIV-1.
Proteins identified in Screens are highlighted in yellow in the Navigator window.
If you select only a HIV Screen dataset, no network can be built, as there is no underlying PPI information.
Q3. How can I start a new search?
A3. Double click any node (protein) in the Navigator window.
OR If your protein of interest is not visible in the presently-loaded network, use the forms boxes in the left panel.
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