HCVpro: Hepatitis C virus protein interaction database

Kwofie, Samuel K.; Schaefer, Ulf; Sundararajan, Vijayaraghava Seshadri; Bajic, Vladimir B.; Christoffels, Alan G.

HCVpro: Hepatitis C virus protein interaction database

Type

Article

Authors

Kwofie, Samuel K.
Schaefer, Ulf
Sundararajan, Vijayaraghava Seshadri
Bajic, Vladimir B.

Christoffels, Alan G.

KAUST Department

Computational Bioscience Research Center (CBRC)
Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
Applied Mathematics and Computational Science Program

Date

2011-12

Abstract

It is essential to catalog characterized hepatitis C virus (HCV) protein-protein interaction (PPI) data and the associated plethora of vital functional information to augment the search for therapies, vaccines and diagnostic biomarkers. In furtherance of these goals, we have developed the hepatitis C virus protein interaction database (HCVpro) by integrating manually verified hepatitis C virus-virus and virus-human protein interactions curated from literature and databases. HCVpro is a comprehensive and integrated HCV-specific knowledgebase housing consolidated information on PPIs, functional genomics and molecular data obtained from a variety of virus databases (VirHostNet, VirusMint, HCVdb and euHCVdb), and from BIND and other relevant biology repositories. HCVpro is further populated with information on hepatocellular carcinoma (HCC) related genes that are mapped onto their encoded cellular proteins. Incorporated proteins have been mapped onto Gene Ontologies, canonical pathways, Online Mendelian Inheritance in Man (OMIM) and extensively cross-referenced to other essential annotations. The database is enriched with exhaustive reviews on structure and functions of HCV proteins, current state of drug and vaccine development and links to recommended journal articles. Users can query the database using specific protein identifiers (IDs), chromosomal locations of a gene, interaction detection methods, indexed PubMed sources as well as HCVpro, BIND and VirusMint IDs. The use of HCVpro is free and the resource can be accessed via http://apps.sanbi.ac.za/hcvpro/ or http://cbrc.kaust.edu.sa/hcvpro/. © 2011 Elsevier B.V.

Citation

Kwofie, S. K., Schaefer, U., Sundararajan, V. S., Bajic, V. B., & Christoffels, A. (2011). HCVpro: Hepatitis C virus protein interaction database. Infection, Genetics and Evolution, 11(8), 1971–1977. doi:10.1016/j.meegid.2011.09.001

Acknowledgements

This work was partly supported by grants from the National Research Foundation (South Africa), National Bioinformatics Network (to S.K.K.) and DST/NRF Research Chair (to A.C. and V.B.B.).