Information Technology Reference
In-Depth Information
x To predict the structure of a protein of unknown structure
6.2 How to Begin
Following the Domains link for any protein in Entrez, one can find the conserved
domains within that protein. The CD-Search
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(or Protein BLAST, with CD-Search
option selected) can be used to find conserved domains (CDs) within a protein. Either the
Accession number, gi number, or the FASTA sequence can be used as a query.
6.3 Alternative Points of Entry
Information on the CDs contained within a protein can also be found from these
databases and tools:
x From any Entrez search: select the
Domains
link to the right of a displayed
record.
x From the Structure Summary page of a MMDB record: this page displays the CDs
within each protein chain immediately below the 3D Domain bar in the graphic
display. Selecting the
CDs
link shows the CD-Search results page.
x From an Entrez Domains search: choose
Domains
from the Entrez
Search
pull-
down menu and enter a search term to retrieve a list of CDs. Clicking on any
resulting CD displays the CD Summary page. The location of this CD in each
aligned protein is indicated by green numerals in the alignment in the bottom
portion of this page.
x From the CDD page: locate CDs by entering text terms into the search box and
proceed as for an Entrez CD search.
x From a BLink report: select the
CDD-Search
button to display the CD-Search
results page.
x From the BLAST main page: follow the RPS-BLAST link to load the CD-Search
page.
6.4 Viewing Conserved Domains
Results from a CD search are displayed as colored bars underneath a sequence ruler.
Moving the mouse over these bars reveals the identity of each domain; domains are also
listed in a format similar to BLAST summary output. Pairwise alignments between the
matched region of the target protein and the representative sequence of each domain are
shown below the bar. Red letters indicate columns with sequence conservation scores
higher than the bits setting in the View Alignment controls, whereas blue letters indicate
residues with conservation scores less than the bit setting.
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[http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi]
