Chem-BLAST Tree is one of the webpages of the HIV Structural Database developed at the National Institute of Standards and Technology (NIST). It provides searches on compounds, inhibitor names, and inhibitor fragments. Chem-BLAST Tree is hierarchical in structure and displays parent-child relationships (data-tree view). The Chem-BLAST Tree looks like the standard Windows Explorer working on folders. It is organized in four levels (Fig. 1):
| - class | |
| - subgroup | |
| - fragment | |
| - compound | |
The Chem-BLAST Tree provides the user a view of relationships between class, subgroup, fragment, and compound. Starting from a class, the user can find a specific subgroup. Subsequently, a list of fragments that contain the requested subgroup can be displayed. Finally, compounds of a specific class, subgroup, and fragment can also be listed.
When the Chem-BLAST Tree page is opened, all of the "class" elements that are available in the 3-D HIV Structural Database (e.g. amino acid, six-member ring) are displayed in the tree in the closed form on the left panel (Fig. 1).
Place the mouse cursor to a plus sign of a specific class (e.g. nitrogen containing), click on the plus sign to see "subgroup" subdirectories (e.g. Subgroup_1, Subgroup_2) of the selected class. This class is now in the opened form 
(Fig. 2)
Click on the "Subgroup_1" element to see the first 50 subgroups that have the "nitrogen containing" class on the right panel
(Fig. 3) .
The Chem-BLAST Tree allows the user to select a subgroup to display fragments that have the selected subgroup of a specific "class" element.
- Click a subgroup element (e.g. cysteine00), 006773_chain1_3 and 045176_chain1_2 fragments are shown on the right panel (Fig. 4). The class (nitrogen containing) and subgroup (cysteine00) information of the displayed fragments are also seen on the top part of the screen.
Find compounds that have a particular class, a specific subgroup, and a fragment can be conducted in the Chem-BLAST Tree.
- Click a fragment (e.g. 006773_chain1_3) to display all of the compound identifiers (Fig. 5) that have the nitrogen class, the cysteine00 subgroup, and the 006773_chain1_3 fragment
To perform an inhibitor search, click a compound identifier (e.g. 1HPX) to open the following page (Fig. 6):
Also the user can view "fragment" subdirectories (e.g Fragment_1, Fragment_2) of the selected "subgroup" folder (Subgroup_1). Each "fragment" folder contains up to 20 fragments that will be displayed on the right panel when the user clicks on a "fragment" folder (Fig. 7).
Along with fragment information, subgroups that are associated with the fragment data are also shown (pink shaded boxes). For instance, both ALA and 028334_chain1_2 fragments have the alanine00 subgroup.
From this page the user can click a fragment (e.g. 006773_chain1_3 ) to see all the compound identifiers (Fig. 5) that have the requested fragment and its associated subgroup (cysteine00)
When the "fragment" element is in the opened form 
, the user can see IDPage subdirectories (e.g. IDPage_1, IDPage_2). Each IDPage folder contains up to ten "ID" elements (e.g. ID_1, ID_2, ID_3). Click on one of these "ID" elements, and compound identifiers including their associated subgroups and fragments information will be displayed on the right panel
(Fig. 8).
The Chem-BLAST Tree allows the user to access to the main webpage of the HIV Structural Database to perform an inhibitor search.
- Click a compound identifier (e.g. 1HPX) to get to the
http://xpdb.nist.gov/hivsdb/hivsdb_fragment_search.pl?GQ=1HPX website (Fig. 6).
Note: Elements represented in blue font (e.g. Subgroup_1) in the Chem-BLAST Tree are clickable.
