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Simple Search
  
For help see below
Help for Search
Structure Map:          
Visualize structure map of virus by providing its NCBI Genome Id. (Eg: NC_006152)

PDB Id:          
Search based on PDB id. (Eg: 1A3R)

Source:           
Search based on source of protein ie;      virus/genus/family/group name. (Eg: Retroviridae/Human Immunodeficiency Virus 1)

Taxon Id:        
Search based NCBI taxonomy id of source organism. (Eg: 11676)

Genome Id:   
Search based on NCBI genome id. (Eg: NC_001802 )

Host:              
Search based on host of virus. (Eg: Homo sapiens)

Protein:          
Search based on protein name or fragment. (Eg: Envelope/ Env/ Gag)

Function:        
Search based on function of protein. GO id should be used. (Eg: 16564/ 16032)

Virion:            
Search based on virus component. GO id should be used. (Eg: 19030 )

Pfam:             
Search based on PFAM id/accession. (Eg: PF00509 / Hemagglutinin )

Scop:            
Search based on SCOP id/domain/fold. (Eg: 23798 / Hemagglutinin)

Cath:              
Search based on CATH id. (Eg: 1.10.530.40 )

Resolution:            
Give the range of resolution as shown in example. ( Eg: 0.5-1)

HOW TO USE

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.

 

b) Question Mark - When question mark is clicked, it gives the precise content to be given for keyword 

search.

  i)For source search it provides with all class,family, sub-family, genus, species and strain names. 

 

     

 ii)For virion search it provides GO term and GO id related to viral components. GO id should be entered in

 the search box of virion. 

    

c) Advanced Search - Click "SEARCH" on top menu bar to go to advanced search.
Following options are seen: 

  

Choose any of the search options given above.

 

II) Result Page: The result page contains total number of hits and all viral proteins corresponding to the 

search options. To get details click on PDB id.

III) Detail Information Page:

a) Description - This section gives the title , Experimental method and the resolution for X-ray diffraction. 

b) 3D structure and PDB file - This section shows the structure image of protein. To visualize structure in

 JMol click on structure image. Also, the Pdb file can be downloaded by clicking on download button.

 

c) Ramachandran plot - This section shows the Ramachandran  plot for PDB structure. Clicking on the 

image opens the detailed plot in pdf format obtained by Procheck. 

d) Genome & Structural Coverage Maps:

 i) 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 mapped on 

genome and total no. of proteins for which available structure is mapped. Then it contains information 

on genes of genome, start & stop positions and protein coded by the genes.

  iii) On the right side of mapping page there are two columns with black lines and orange blocks.

 (1) First column maps proteins to genome where black line is genome and orange block is protein

 organized according to its position on genome.

 

(2) Second 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

 fragment of protein with known structure is very small, then red block may not be visible. To see BLAST

 result click "i". To check the protein structure click the PDB chain id given.

  e) Other 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.

 

f) Cross Database links:

This section contains link to Procheck, PDBe, PDBSum, ProFunc and Evolutionary Trace servers.