I) Using retrieval utilities:
a) Simple Search - The column for simple search is given on left of each page. It includes several search
options like PDB id, taxonomy id, genome id, source
organism, protein family etc.
Mark - When question mark is clicked, it gives
the precise content to be given for keyword
source search it provides with all class,family,
sub-family, genus, species and strain names.
virion search it provides GO term and GO id related to
viral components. GO id should be entered in
search box of virion.
c) Advanced Search
- Click "SEARCH" on top menu bar to go to advanced search.
Following options are seen:
of the search options given above.
II) Result Page: The result page contains total number of hits and all viral
proteins corresponding to the
To get details click on PDB id.
Description - This section gives the title ,
Experimental method and the resolution for X-ray
structure and PDB file - This section shows the structure
image of protein. To visualize structure in
on structure image. Also, the Pdb file can be
downloaded by clicking on download button.
plot - This section shows the Ramachandran
plot for PDB structure. Clicking on the
the detailed plot in pdf format obtained by Procheck.
& Structural Coverage Maps:
The topmost part of detail page contains a link named
as **Genome & SCM**. This link takes us to the
genome of the protein source organism genome id.
ii) To go
for structure map click on Genome Id. The top of
mapping page provides information viz.
Genome Id, virus name,genome length,
percent structural coverage, total no. of proteins
genome and total no. of proteins for which
available structure is mapped. Then it contains
on genes of genome, start & stop
protein coded by the genes.
On the right side of mapping page there are two
columns with black lines and orange blocks.
First column maps proteins to genome where black line
is genome and orange block is protein
according to its position on genome.
column maps protein structure to the whole protein
where orange block is entire protein and
red block is
the fragment of protein with known structure organized
according to the BLAST result. If the
of protein with known structure is very small, then
red block may not be visible. To see BLAST
click "i". To check the protein structure
click the PDB chain id given.
Information on Detail Page: Detail page
contains information on chains of protein, ligands,
secondary structure (H-helix, G-3 10 helix, E-sheet, T-turn,
S-bend, B- isolated residue in beta bridge), epitope,
ramachandran plot of entire protein as well as all
chains, GO terms to depict the function &
component of protein, domains and reference.
Cross Database links:
section contains link to Procheck, PDBe, PDBSum,
ProFunc and Evolutionary Trace servers.