ViPs   -   Viral    Protein   Structure   resource

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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)

Three-dimensional structure of protein provides information pertaining to biological mechanism, function, interactions, and hereby, has significant implications in designing anti-viral drugs and protein-based vaccines. Due to the heterogeneity of existing structure databases, there is a need to develop a dedicated database of viral protein structures.

"ViPs" is a relational database of all known protein structures of virus, either experimentally determined using X-ray diffraction/NMR or predicted by homology modelling. The database has two aspects:
  • First one includes structure data of viral proteins from PDB archive, which is organised according to the taxonomic hierarchy. This resource provides detailed information on coordinates, secondary structure, primary sequence, domain, GO terms, taxonomy, host, literature & cross-references to relevant databases.
  • Second aspect renders structure map that links viral genome to its structural proteome. The map organizes gene, its coded protein/polyprotein and the structure of that protein,if present, on the genome. Map serves the purpose of providing the extent of structural coverage and to keep track of the proteins or families to which much attention is paid.

The resource contains retrieval utilities based on virus name, host, function, virion, domain, resolution and NCBI genome id. Data mining tools are embedded for sequence and structure analysis, viz. sequence or structure alignment, structure search based on homology, quality check, visualization, and superimposition. The database provides both conformational and sequential epitopes for each chain of the protein.

Comments/Suggestions : smita@bioinfo.net.in

ViPs has been developed at Bioinformatics Centre, University of Pune, funded by Ministry of Communications and Information Technology, Government of India.

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