Information Technology Reference
In-Depth Information
By using the full array of Entrez search tools, the resulting list of MMDB records
can be honed, ideally, to a workable list from which a record can be selected. Users
should note that multiple records may exist for a given protein, reflecting different
experimental techniques, conditions, and the presence or absence of various ligands or
metal ions. Records may also contain different fragments of the full-length molecule. In
addition, many structures of mutant proteins are also available. The PDB record for a
given structure generally contains some description of the experimental conditions under
which the structure was determined, and this file can be accessed by selecting the PDB
code link at the top of the Structure Summary page.
4.3 Alternative Points of Entry
Structure Summary pages can also be found from the following NCBI databases and
tools:
x Select the Structure
links
to the right of any Entrez record found; records with
Structure links can also be located by choosing
Structure links
from the
Display
pull-down menu.
x Select the
Related Sequences
link to the right of an Entrez record to find proteins
related by sequence similarity, and then select
Structure links
in the
Display
pull-
down menu.
x Choose the PDB database from a blastp (protein-protein BLAST) search; only
sequences with structure records will be retrieved by BLAST. The
Related
Structures
link provides 3D views in Cn3D.
x Select the
3D Structures
button on any BLink report to show those BLAST hits
for which structural data are available.
From the results of any protein BLAST search, click on a red 'S' linkout to view
the sequence alignment with a structure record.
x
4.4 Viewing 3D Structures
3D Domains.
The 3D domains of a protein are displayed on the Structure Summary page.
It is useful to know how many 3D domains a protein contains and whether they are
continuous in sequence when viewing the full 3D structure of the molecule.
Secondary Structure.
Knowing the secondary structure of a protein can also be a
useful prelude to viewing the 3D structure of the molecule. The secondary structure can
be viewed easily by first selecting the
Protein
link to the left of the desired chain in the
graphic display. Finding oneself in Entrez Protein, selecting
Graphics
in the Display pull-
down menu presents secondary structure diagrams for the molecule.
Full Protein Structures.
Cn3D is a software package for displaying 3D structures
of proteins. Once it has been installed
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and the Internet browser has been configured
correctly, simply selecting the
View 3D Structure
button on a Structure Summary page
launches the application. Once the structure is loaded, a user can manipulate and
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[http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3dinstall.shtml]