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VIP DB--a viral protein domain usage and distribution database.
Ting-Wen Chen1, Richie Ruei-Chi Gan, Timothy H Wu
1Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan. g39328001@ym.edu.tw
Genomics
|June 28, 2012
Summary
A new database, VIP DB, links viral proteins to potential functions and interactions by analyzing protein domains. This resource aids researchers in understanding viral protein roles during infection and replication.
Area of Science:
- Virology
- Bioinformatics
- Computational Biology
Background:
- Viral proteins play crucial roles in infection and replication.
- Understanding viral protein functions and interactions is essential but often challenging.
- Many viral proteins' functions and interaction partners remain unexplored.
Purpose of the Study:
- To create a comprehensive database, the VIral Protein domain DataBase (VIP DB).
- To associate viral proteins with their putative functions and interaction partners.
- To facilitate the exploration of viral protein roles in host-pathogen interactions.
Main Methods:
- Systematic assignment of protein domains from viral proteins.
- Inference of protein functions and interaction partners based on domain annotations.
- Correlation of domain information with Gene Ontology (GO) classification, KEGG pathways, and domain-domain interactions.
Main Results:
- The VIP DB contains 2,322 unique domains from 2,404 viruses.
- 42.7% of domains have GO records, 39.6% have domain-domain interaction records.
- 26.3% of domains are also found in mammals or plants, suggesting potential host interactions.
Conclusions:
- The VIP DB serves as a valuable resource for virologists.
- It aids in identifying potential roles and functions of viral proteins.
- The database promotes further research into viral protein mechanisms and host interactions.
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