Manual of the HTP server
Entry Viewer Panel
This panel is for summarize the information collected and/or predicted for each protein
in the human proteome. The screenshot of an example Entry Viewer Panel is in the right side, the
main areas are the following:
- The UniProt name of the protein.
- Navigation panel. In the middle there is the HTP code of the given entry.
The meanings of the components from left to right are
- Link to the first entry in the current search result list
- Link to the previous entry in the current result list
- Label containing HTP code of the given entry
- Link to the next entry in the current result list
- Link to the last entry in the current result list
-
PDB cross references of the given entry. By clicking the codes, user can select
each PDB entry for visualization.
Note, this area is visible for entries of which evidence type is 3D.
-
Main area. The content of this panel depends on the selected tab, which are the following:
- Summary tab
It contains basic informations about the entry, such as gene name,
cross references, reliability of the predicted topology, number of transmembrane segments,
and the download buttons for getting the xml file of the given entry.
- 1D tab
It contains the color-coded amino acid sequence of the given human transmembrane protein
based on the determined or predicted topology (red: inside/cytosolic;
yellow: membrane; orange: re-entrant loop; blue: outside/extra-cytosolic region).
- 2D tab
It contains a graphical representation of the determined and predicted topology of
the given entry. The graph consists of three parts: the results of the final HTP prediction,
the results of the various topology and topography prediction methods and the collected
constraints aligned to the amino acid sequence of the given entry.
The x-axes on the graph are the sequence, lower red lines represent inside/cytosolic regions,
yellow rectangles code transmembrane regions, orange rectangles show membrane re-entrant loops
and upper blue lines represent outside/extra-cytosolic regions. Thin gray lines indicate regions,
where the topology information is not predicted/determined.
- 3D tab
This tab is selectable for entries of which have the evidence level 3D. It contains
the 3D representation of the structure of the given entry positioned in the membrane
bilayer. For the 3D representation, the
Open Astex Viewer is used. The membrane
orientation is determined by the TMDET algorithm.
Data are taken from PDBTM database.
- XML
This tab shows the raw xml description of the given entry. The XSD schema definition
for the xml files can be found here.
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