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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
Interactive protein display page for Tat in HIVToolbox.Sequence window, Structure windows, Log windows, and Sequence Alignment section of HIVToolbox are shown. The interactive results page for HIV-1 tat is shown. The scrollable sequence window shows the protein sequence, domains (with colored fonts), functional residues (highlighted), protein-protein interaction sites (thin lines under sequence), mapped protein structures (thin colored lines over sequence) and minimotifs (figures under sequence). The synchronized interactive structural displays show domains and selected minimotifs (left panel), functional sites and selected protein-protein interaction sites (center panel), and residues conserved at or above a sequence conservation threshold selected with a slider or text box (right panel). The Sequence Alignment section shows alignment of a representative set of 20 sequences with the RefSeq sequence and the structure sequence. A second tab reveals a position specific-scoring matrix of amino acid frequencies at each position in the protein. More details about the features and use of HIVToolbox are in the supplement, and video tutorials are at Bio-Toolkit [http://www.bio-toolkit.com].
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pone-0020122-g009: Interactive protein display page for Tat in HIVToolbox.Sequence window, Structure windows, Log windows, and Sequence Alignment section of HIVToolbox are shown. The interactive results page for HIV-1 tat is shown. The scrollable sequence window shows the protein sequence, domains (with colored fonts), functional residues (highlighted), protein-protein interaction sites (thin lines under sequence), mapped protein structures (thin colored lines over sequence) and minimotifs (figures under sequence). The synchronized interactive structural displays show domains and selected minimotifs (left panel), functional sites and selected protein-protein interaction sites (center panel), and residues conserved at or above a sequence conservation threshold selected with a slider or text box (right panel). The Sequence Alignment section shows alignment of a representative set of 20 sequences with the RefSeq sequence and the structure sequence. A second tab reveals a position specific-scoring matrix of amino acid frequencies at each position in the protein. More details about the features and use of HIVToolbox are in the supplement, and video tutorials are at Bio-Toolkit [http://www.bio-toolkit.com].

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)

Interactive protein display page for Tat in HIVToolbox.Sequence window, Structure windows, Log windows, and Sequence Alignment section of HIVToolbox are shown. The interactive results page for HIV-1 tat is shown. The scrollable sequence window shows the protein sequence, domains (with colored fonts), functional residues (highlighted), protein-protein interaction sites (thin lines under sequence), mapped protein structures (thin colored lines over sequence) and minimotifs (figures under sequence). The synchronized interactive structural displays show domains and selected minimotifs (left panel), functional sites and selected protein-protein interaction sites (center panel), and residues conserved at or above a sequence conservation threshold selected with a slider or text box (right panel). The Sequence Alignment section shows alignment of a representative set of 20 sequences with the RefSeq sequence and the structure sequence. A second tab reveals a position specific-scoring matrix of amino acid frequencies at each position in the protein. More details about the features and use of HIVToolbox are in the supplement, and video tutorials are at Bio-Toolkit [http://www.bio-toolkit.com].
© Copyright Policy
Related In: Results  -  Collection

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

pone-0020122-g009: Interactive protein display page for Tat in HIVToolbox.Sequence window, Structure windows, Log windows, and Sequence Alignment section of HIVToolbox are shown. The interactive results page for HIV-1 tat is shown. The scrollable sequence window shows the protein sequence, domains (with colored fonts), functional residues (highlighted), protein-protein interaction sites (thin lines under sequence), mapped protein structures (thin colored lines over sequence) and minimotifs (figures under sequence). The synchronized interactive structural displays show domains and selected minimotifs (left panel), functional sites and selected protein-protein interaction sites (center panel), and residues conserved at or above a sequence conservation threshold selected with a slider or text box (right panel). The Sequence Alignment section shows alignment of a representative set of 20 sequences with the RefSeq sequence and the structure sequence. A second tab reveals a position specific-scoring matrix of amino acid frequencies at each position in the protein. More details about the features and use of HIVToolbox are in the supplement, and video tutorials are at Bio-Toolkit [http://www.bio-toolkit.com].
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