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.
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