BioAfrica's HIV-1 proteomics resource: combining protein data with bioinformatics tools.
Most Internet online resources for investigating HIV biology contain either bioinformatics tools, protein information or sequence data. The objective of this study was to develop a comprehensive online proteomics resource that integrates bioinformatics with the latest information on HIV-1 protein structure, gene expression, post-transcriptional/post-translational modification, functional activity, and protein-macromolecule interactions. The BioAfrica HIV-1 Proteomics Resource http://bioafrica.mrc.ac.za/proteomics/index.html is a website that contains detailed information about the HIV-1 proteome and protease cleavage sites, as well as data-mining tools that can be used to manipulate and query protein sequence data, a BLAST tool for initiating structural analyses of HIV-1 proteins, and a proteomics tools directory. The Proteome section contains extensive data on each of 19 HIV-1 proteins, including their functional properties, a sample analysis of HIV-1HXB2, structural models and links to other online resources. The HIV-1 Protease Cleavage Sites section provides information on the position, subtype variation and genetic evolution of Gag, Gag-Pol and Nef cleavage sites. The HIV-1 Protein Data-mining Tool includes a set of 27 group M (subtypes A through K) reference sequences that can be used to assess the influence of genetic variation on immunological and functional domains of the protein. The BLAST Structure Tool identifies proteins with similar, experimentally determined topologies, and the Tools Directory provides a categorized list of websites and relevant software programs. This combined database and software repository is designed to facilitate the capture, retrieval and analysis of HIV-1 protein data, and to convert it into clinically useful information relating to the pathogenesis, transmission and therapeutic response of different HIV-1 variants. The HIV-1 Proteomics Resource is readily accessible through the BioAfrica website at: http://bioafrica.mrc.ac.za/proteomics/index.html.
Doherty
Ryan S
RS
Molecular Virology and Bioinformatics Unit, Africa Centre for Health and Population Studies, Doris Duke Medical Research Institute, Nelson R, Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa. rsd@ncf.ca
De Oliveira
Tulio
T
Seebregts
Chris
C
Danaviah
Sivapragashini
S
Gordon
Michelle
M
Cassol
Sharon
S
D000349:Africa; D019295:Computational Biology; D030562:Databases, Protein; D015870:Gene Expression; D015497:HIV-1 / Q000235:genetics / Q000378:metabolism* / Q000472:pathogenicity; D006801:Humans; D020407:Internet; D011499:Protein Processing, Post-Translational; D020543:Proteome; D040901:Proteomics; D012984:Software; D014764:Viral Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism
D020543:Proteome; D014764:Viral Proteins