Information Technology Reference
In-Depth Information
with structure neighbors in Cn3D. When this process is complete, the record is assigned a
unique Accession number, the MMDB-ID (Appendix 1), while also retaining the original
four-character PDB code
.
Figure 2: The Structure Summary page.
The page consists of three parts: the header, the view bar, and
the graphic display. The header contains basic identifying information about the record: a description of the
protein (
Description:
), the author list (
Deposition:
), the species of origin (
Taxonomy:
), literature references
(
Reference:
), the MMDB-ID (
MMDB:
), and the PDB code (
PDB:
). Several of these data serve as links to
additional information. For example, the species name links to the Taxonomy browser, the literature
references link to PubMed, and the PDB code links to the PDB Web site. The view bar allows the user to
view the structure record either as a graphic with Cn3D or as a text record in either ASN.1, PDB (RasMol),
or Mage formats. The latter can also be downloaded directly from this page. The graphic display contains a
variety of information and links to related databases: (
a
) The Chain bar. Each chain of the molecule is
displayed as a
dark bar
labeled with residue numbers. To the
left
of this bar is a
Protein
hyperlink that
takes the user to a view of the protein record in Entrez Protein. The bar itself is also a hyperlink and
displays the VAST neighbors of the chain. If a structure contains nucleotide sequences, they are displayed
in the order contained in the PDB record. A
Nucleotide
hyperlink to their
left
takes the user to the
appropriate record in Entrez Nucleotide. (
b
) The VAST (3D) Domain bar. The
colored bars
immediately
below the Chain bar indicate the locations of structural domains found by the original MMDB processing
of the protein. In many cases, such a domain contains unconnected sections of the protein sequence, and in
such cases, discontinuous pieces making up the domain will have bars of the same color. To the
left
of the
Domain bar is a 3D Domains hyperlink (
3d Domains
) that launches the 3D Domains browser in Entrez,
where the user can find information about each constituent domain. Selecting a colored segment displays
the VAST Structure Neighbors page for that domain. (
c
) The CD bar. Below the VAST Domain bar are
rounded, rectangular bars
representing conserved domains found by a CD-Search. The bars identify the
best scoring hits; overlapping hits are shown only if the mutual overlap with hits having better scores is less
than 50%. The
CDs
hyperlink to the
left
of the bar displays the CD records in Entrez Domains. Each of the
colored bars is also a hyperlink that displays the corresponding CD Summary page configured to show the
multiple alignment of the protein sequence with members of the selected CD.
