Limits...
HIVToolbox, an integrated web application for investigating HIV.

Sargeant D, Deverasetty S, Luo Y, Villahoz Baleta A, Zobrist S, Rathnayake V, Russo JC, Vyas J, Muesing MA, Schiller MR - PLoS ONE (2011)

Bottom Line: HIV-1 integrase protein was used as a case study to show the utility of this application.We show how data integration facilitates identification of new questions and hypotheses much more rapid and convenient than current approaches using isolated repositories.Several new hypotheses for integrase were created as an example, and we experimentally confirmed a predicted CK2 phosphorylation site.

View Article: PubMed Central - PubMed

Affiliation: School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America.

ABSTRACT
Many bioinformatic databases and applications focus on a limited domain of knowledge federating links to information in other databases. This segregated data structure likely limits our ability to investigate and understand complex biological systems. To facilitate research, therefore, we have built HIVToolbox, which integrates much of the knowledge about HIV proteins and allows virologists and structural biologists to access sequence, structure, and functional relationships in an intuitive web application. HIV-1 integrase protein was used as a case study to show the utility of this application. We show how data integration facilitates identification of new questions and hypotheses much more rapid and convenient than current approaches using isolated repositories. Several new hypotheses for integrase were created as an example, and we experimentally confirmed a predicted CK2 phosphorylation site. Weblink: [http://hivtoolbox.bio-toolkit.com].

Show MeSH

Related in: MedlinePlus

Protein selection page of the HIVToolbox website.An image of the Introduction page of HIVToolbox is shown. Selection of any HIV-1 protein name or protein object launches an interactive results page about the protein. A drop-down menu is provided for non-graphical access to proteins.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC3102074&req=5

pone-0020122-g008: Protein selection page of the HIVToolbox website.An image of the Introduction page of HIVToolbox is shown. Selection of any HIV-1 protein name or protein object launches an interactive results page about the protein. A drop-down menu is provided for non-graphical access to proteins.

Mentions: The basic workflow for HIVToolbox is as follows: At the application's introductory webpage, users can select the HIV-1 protein they wish to investigate from a diagram of the HIV-1 life cycle (Fig. 8). The application then displays the primary interface, an interactive console from which the user can perform a variety of functions related to the sequences, structures, and functions of the selected protein (Fig. 9). Alternatively, the primary interface page can be accessed directly via links in the HIV-1 protein structure pages at the Protein Data Bank, which pre-loads the selected structure.


HIVToolbox, an integrated web application for investigating HIV.

Sargeant D, Deverasetty S, Luo Y, Villahoz Baleta A, Zobrist S, Rathnayake V, Russo JC, Vyas J, Muesing MA, Schiller MR - PLoS ONE (2011)

Protein selection page of the HIVToolbox website.An image of the Introduction page of HIVToolbox is shown. Selection of any HIV-1 protein name or protein object launches an interactive results page about the protein. A drop-down menu is provided for non-graphical access to proteins.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3102074&req=5

pone-0020122-g008: Protein selection page of the HIVToolbox website.An image of the Introduction page of HIVToolbox is shown. Selection of any HIV-1 protein name or protein object launches an interactive results page about the protein. A drop-down menu is provided for non-graphical access to proteins.
Mentions: The basic workflow for HIVToolbox is as follows: At the application's introductory webpage, users can select the HIV-1 protein they wish to investigate from a diagram of the HIV-1 life cycle (Fig. 8). The application then displays the primary interface, an interactive console from which the user can perform a variety of functions related to the sequences, structures, and functions of the selected protein (Fig. 9). Alternatively, the primary interface page can be accessed directly via links in the HIV-1 protein structure pages at the Protein Data Bank, which pre-loads the selected structure.

Bottom Line: HIV-1 integrase protein was used as a case study to show the utility of this application.We show how data integration facilitates identification of new questions and hypotheses much more rapid and convenient than current approaches using isolated repositories.Several new hypotheses for integrase were created as an example, and we experimentally confirmed a predicted CK2 phosphorylation site.

View Article: PubMed Central - PubMed

Affiliation: School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America.

ABSTRACT
Many bioinformatic databases and applications focus on a limited domain of knowledge federating links to information in other databases. This segregated data structure likely limits our ability to investigate and understand complex biological systems. To facilitate research, therefore, we have built HIVToolbox, which integrates much of the knowledge about HIV proteins and allows virologists and structural biologists to access sequence, structure, and functional relationships in an intuitive web application. HIV-1 integrase protein was used as a case study to show the utility of this application. We show how data integration facilitates identification of new questions and hypotheses much more rapid and convenient than current approaches using isolated repositories. Several new hypotheses for integrase were created as an example, and we experimentally confirmed a predicted CK2 phosphorylation site. Weblink: [http://hivtoolbox.bio-toolkit.com].

Show MeSH
Related in: MedlinePlus