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{"title"=>"HIVToolbox, an integrated web application for investigating HIV", "type"=>"journal", "authors"=>[{"first_name"=>"David", "last_name"=>"Sargeant", "scopus_author_id"=>"36605085500"}, {"first_name"=>"Sandeep", "last_name"=>"Deverasetty", "scopus_author_id"=>"38361386700"}, {"first_name"=>"Yang", "last_name"=>"Luo", "scopus_author_id"=>"55712643700"}, {"first_name"=>"Angel Villahoz", "last_name"=>"Baleta", "scopus_author_id"=>"53871149700"}, {"first_name"=>"Stephanie", "last_name"=>"Zobrist", "scopus_author_id"=>"40762771300"}, {"first_name"=>"Viraj", "last_name"=>"Rathnayake", "scopus_author_id"=>"36661456900"}, {"first_name"=>"Jacqueline C.", "last_name"=>"Russo", "scopus_author_id"=>"40762244900"}, {"first_name"=>"Jay", "last_name"=>"Vyas", "scopus_author_id"=>"24831420400"}, {"first_name"=>"Mark A.", "last_name"=>"Muesing", "scopus_author_id"=>"6701702393"}, {"first_name"=>"Martin R.", "last_name"=>"Schiller", "scopus_author_id"=>"7101808538"}], "year"=>2011, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "scopus"=>"2-s2.0-79957476320", "pui"=>"361822339", "doi"=>"10.1371/journal.pone.0020122", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "sgr"=>"79957476320", "pmid"=>"21647445"}, "id"=>"49f6433e-822c-39a5-9235-5d3bf8172587", "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].", "link"=>"http://www.mendeley.com/research/hivtoolbox-integrated-web-application-investigating-hiv", "reader_count"=>20, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>1, "Librarian"=>1, "Student > Doctoral Student"=>2, "Researcher"=>7, "Student > Ph. D. Student"=>4, "Other"=>2, "Student > Bachelor"=>2, "Lecturer"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>1, "Librarian"=>1, "Student > Doctoral Student"=>2, "Researcher"=>7, "Student > Ph. D. Student"=>4, "Other"=>2, "Student > Bachelor"=>2, "Lecturer"=>1}, "reader_count_by_subject_area"=>{"Engineering"=>1, "Biochemistry, Genetics and Molecular Biology"=>2, "Agricultural and Biological Sciences"=>8, "Medicine and Dentistry"=>1, "Business, Management and Accounting"=>1, "Chemistry"=>1, "Social Sciences"=>1, "Computer Science"=>5}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Chemistry"=>{"Chemistry"=>1}, "Social Sciences"=>{"Social Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>8}, "Computer Science"=>{"Computer Science"=>5}, "Business, Management and Accounting"=>{"Business, Management and Accounting"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>2}}, "reader_count_by_country"=>{"Argentina"=>1, "United States"=>1, "Portugal"=>1, "Germany"=>1, "India"=>1}, "group_count"=>0}

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• http://doi.org/10.1371/journal.pone.0092877
• http://doi.org/10.1371/journal.pone.0098810
• http://doi.org/10.1093/nar/gkr1189
• http://doi.org/10.1016/j.drudis.2012.02.015
• http://doi.org/10.1093/nar/gku1126

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• {"title"=>"HIVToolbox", "url"=>"http://en.wikipedia.org/wiki/HIVToolbox", "timestamp"=>"2018-08-19T23:37:05Z"}

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Figshare

• {"files"=>["https://ndownloader.figshare.com/files/771885"], "description"=>"<p>Output of HIVToolbox showing spatial positions on surface plots of different function sites on IN structural models in the same orientation. (<b>A</b>) Models of IN dimers showing domains (left panel), several functional sites (middle panel) and residues >98% conserved (right panel, yellow). In the left panel the yellow numbers indicate the monomer subunit for each domain. In the middle panel residues are colored as follows: DNA binding residues = green, tetramerization residues = blue, active site residues = royal blue (<b>B</b>) IN:LEDGF hetero-tetramer showing LEDGF domains (grey) and proposed viral LTR binding groove (arrowhead) (<b>C</b>) IN dimer showing nuclear import motifs.</p>", "links"=>[], "tags"=>["integrase", "dimers"], "article_id"=>442252, "categories"=>["Information And Computing Sciences", "Biological Sciences"], "users"=>["David Sargeant", "Sandeep Deverasetty", "Yang Luo", "Angel Villahoz Baleta", "Stephanie Zobrist", "Viraj Rathnayake", "Jacqueline C. Russo", "Jay Vyas", "Mark A. Muesing", "Martin R. Schiller"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0020122.g002", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Analysis_of_Integrase_model_dimers_hetero_tetramers_/442252", "title"=>"Analysis of Integrase model dimers hetero-tetramers.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 18:08:03"}
• {"files"=>["https://ndownloader.figshare.com/files/772587"], "description"=>"<p>An image of the <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0020122#s1\" target=\"_blank\">Introduction</a> 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.</p>", "links"=>[], "tags"=>["hivtoolbox"], "article_id"=>442953, "categories"=>["Information And Computing Sciences", "Biological Sciences"], "users"=>["David Sargeant", "Sandeep Deverasetty", "Yang Luo", "Angel Villahoz Baleta", "Stephanie Zobrist", "Viraj Rathnayake", "Jacqueline C. Russo", "Jay Vyas", "Mark A. Muesing", "Martin R. Schiller"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0020122.g008", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Protein_selection_page_of_the_HIVToolbox_website_/442953", "title"=>"Protein selection page of the HIVToolbox website.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 18:11:47"}
• {"files"=>["https://ndownloader.figshare.com/files/772703"], "description"=>"<p>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 [<a href=\"http://www.bio-toolkit.com\" target=\"_blank\">http://www.bio-toolkit.com</a>].</p>", "links"=>[], "tags"=>["tat"], "article_id"=>443069, "categories"=>["Information And Computing Sciences", "Biological Sciences"], "users"=>["David Sargeant", "Sandeep Deverasetty", "Yang Luo", "Angel Villahoz Baleta", "Stephanie Zobrist", "Viraj Rathnayake", "Jacqueline C. Russo", "Jay Vyas", "Mark A. Muesing", "Martin R. Schiller"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0020122.g009", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Interactive_protein_display_page_for_Tat_in_HIVToolbox_/443069", "title"=>"Interactive protein display page for Tat in HIVToolbox.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 18:12:26"}
• {"files"=>["https://ndownloader.figshare.com/files/772278"], "description"=>"<p>(<b>A</b>) Phosphorylation of IN by CK2. Reactions containing IN, ³²P-γ-ATP and CK2 were serially diluted 1∶3 starting from 50 U/mL (right lane). The extent of phosphorylation was visualized by SDS-PAGE and autoradiography. (<b>B</b>) Phosphorylation of IN domains by CK2. Reactions as in A and contained purified GST-IN or GST-IN domains as indicated in the diagram. IN(S283A) is a point mutation of one of the putative CKII phosphorylation sites. (<b>C</b>) His-tagged point mutants of putative CKII sites within IN were phosphorylated by CK2 as in (A). A control reaction lacking IN showed no phosphorylation (not shown). Reduced phosphorylation of S283A mutant is indicated (*). Samples were normalized for protein concentration.</p>", "links"=>[], "tags"=>["phosphorylated", "ckii", "serine"], "article_id"=>442644, "categories"=>["Information And Computing Sciences", "Biological Sciences"], "users"=>["David Sargeant", "Sandeep Deverasetty", "Yang Luo", "Angel Villahoz Baleta", "Stephanie Zobrist", "Viraj Rathnayake", "Jacqueline C. Russo", "Jay Vyas", "Mark A. Muesing", "Martin R. Schiller"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0020122.g005", "stats"=>{"downloads"=>2, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Integrase_is_phosphorylated_by_CKII_on_serine_283_/442644", "title"=>"Integrase is phosphorylated by CKII on serine 283.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 18:10:05"}
• {"files"=>["https://ndownloader.figshare.com/files/772390"], "description"=>"<p>Boxes show different tables (titles listed on top row) and a description. Foreign keys between tables are shown.</p>", "links"=>[], "tags"=>["diagram", "hivtoolbox", "mysql"], "article_id"=>442749, "categories"=>["Information And Computing Sciences", "Biological Sciences"], "users"=>["David Sargeant", "Sandeep Deverasetty", "Yang Luo", "Angel Villahoz Baleta", "Stephanie Zobrist", "Viraj Rathnayake", "Jacqueline C. Russo", "Jay Vyas", "Mark A. Muesing", "Martin R. Schiller"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0020122.g006", "stats"=>{"downloads"=>1, "page_views"=>25, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Entity_Relationship_diagram_of_HIVToolbox_model_as_a_MySQL_database_/442749", "title"=>"Entity Relationship diagram of HIVToolbox model as a MySQL database.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 18:10:40"}
• {"files"=>["https://ndownloader.figshare.com/files/772473"], "description"=>"<p>Diagram of software architecture of HIVToolbox.</p>", "links"=>[], "tags"=>["Computational biology", "computer science"], "article_id"=>442836, "categories"=>["Information And Computing Sciences", "Biological Sciences"], "users"=>["David Sargeant", "Sandeep Deverasetty", "Yang Luo", "Angel Villahoz Baleta", "Stephanie Zobrist", "Viraj Rathnayake", "Jacqueline C. Russo", "Jay Vyas", "Mark A. Muesing", "Martin R. Schiller"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0020122.g007", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Diagram_of_software_architecture_of_HIVToolbox_/442836", "title"=>"Diagram of software architecture of HIVToolbox.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 18:11:10"}
• {"files"=>["https://ndownloader.figshare.com/files/772860"], "description"=>"<p>Statistics for data in the HIVToolbox database.</p>", "links"=>[], "tags"=>["hivtoolbox"], "article_id"=>443229, "categories"=>["Information And Computing Sciences", "Biological Sciences"], "users"=>["David Sargeant", "Sandeep Deverasetty", "Yang Luo", "Angel Villahoz Baleta", "Stephanie Zobrist", "Viraj Rathnayake", "Jacqueline C. Russo", "Jay Vyas", "Mark A. Muesing", "Martin R. Schiller"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0020122.t003", "stats"=>{"downloads"=>0, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Statistics_for_data_in_the_HIVToolbox_database_/443229", "title"=>"Statistics for data in the HIVToolbox database.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-20 18:13:22"}
• {"files"=>["https://ndownloader.figshare.com/files/771754"], "description"=>"<p>(<b>A–C</b>) Output of HIVToolbox showing relationships of IN elements shown in a model constructed from superposition of the catalytic domains in structures 1EX4 and 1K6Y. Residues 1–7, 47–55, 140–148, and 270–288 are unstructured and not shown. The left panels shows domains [NTD (red), CCD (Blue), and CTD (green)] and minimotifs; the center panels show functional sites and protein-protein interactions the right panels shows residues that are >98% conserved in 3787 HIV-1 IN isolates (yellow). (<b>A</b>) Location of three of the four putative CK2 phosphorylation sites located on the surface of the IN CCD (left panel); the 4^th CK2 site is in the CTD unstructured region. Numbers indicate the positions of putative phosphorylation sites. D270 is the last residue in the structure (orange). Conservation of the residues on CK2 sites is shown in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0020122#pone-0020122-t001\" target=\"_blank\"><b>Table 1</b></a>. (<b>B</b>) Conservation and location of the dimerization interface(s). Residues at the dimerization interface less than 3.25 Å from atoms in the other chain are colored: (red, 1EX4), (cyan, 1WJA), and (lighter cyan, 1K6Y). (<b>B, C</b>) Conservation and location of protein-protein interaction sites, modification sites, and DNA binding sites. (<b>C</b>) is a 180° rotation of (<b>B</b>) about the z-axis. (<b>A, B, C</b>) Sites are colored: DNA binding = green, Importin 7 binding = dark purple and dark green, Zn binding = purple, Karyopherin α5 binding = teal and orange, LEDGF binding = teal, Lysine acetylation = dark green, proline isomerization = orange, active site = royal blue, reverse transcriptase (RT) binding = brown.</p>", "links"=>[], "tags"=>["integrase"], "article_id"=>442108, "categories"=>["Information And Computing Sciences", "Biological Sciences"], "users"=>["David Sargeant", "Sandeep Deverasetty", "Yang Luo", "Angel Villahoz Baleta", "Stephanie Zobrist", "Viraj Rathnayake", "Jacqueline C. Russo", "Jay Vyas", "Mark A. Muesing", "Martin R. Schiller"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0020122.g001", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Analysis_of_Integrase_with_HIVToolbox_/442108", "title"=>"Analysis of Integrase with HIVToolbox.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 18:07:17"}
• {"files"=>["https://ndownloader.figshare.com/files/772890"], "description"=>"<p>*Sequence features that are multimerization interfaces were calculated in Molmol based on residues that were less than 3.25 Å away from at least one residue in another subunit <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0020122#pone.0020122-Koradi1\" target=\"_blank\">[63]</a>.</p>", "links"=>[], "tags"=>["hivtoolbox", "mysql"], "article_id"=>443257, "categories"=>["Information And Computing Sciences", "Biological Sciences"], "users"=>["David Sargeant", "Sandeep Deverasetty", "Yang Luo", "Angel Villahoz Baleta", "Stephanie Zobrist", "Viraj Rathnayake", "Jacqueline C. Russo", "Jay Vyas", "Mark A. Muesing", "Martin R. Schiller"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0020122.t002", "stats"=>{"downloads"=>5, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Sources_of_data_in_the_HIVToolbox_MySQL_database_/443257", "title"=>"Sources of data in the HIVToolbox MySQL database.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-20 18:13:33"}
• {"files"=>["https://ndownloader.figshare.com/files/772043"], "description"=>"<p>Output of HIVToolbox showing surface plots of IN structural models. (<b>A, B</b>) IN tetramers showing domain organization (left panels) and locations of actives site residues (royal blue), proposed viral DNA binding grooves (yellow lines), proposed genomic DNA binding channel (red line), and zinc binding sites (cyan). Yellow numbers indicate the subunit too which the domain belongs. (<b>C</b>) IN:LEDGF hetero-octamers models showing organization of proteins (left panel) and proposed DNA binding groove (middle panel, red line). LEDGF subunits are colored grey. (<b>D</b>) An end-on view of the proposed host DNA binding channel in the IN:LEGDF hetero-octamer model shown in (<b>C</b>) (red circle).</p>", "links"=>[], "tags"=>["integrase", "tetramers"], "article_id"=>442410, "categories"=>["Information And Computing Sciences", "Biological Sciences"], "users"=>["David Sargeant", "Sandeep Deverasetty", "Yang Luo", "Angel Villahoz Baleta", "Stephanie Zobrist", "Viraj Rathnayake", "Jacqueline C. Russo", "Jay Vyas", "Mark A. Muesing", "Martin R. Schiller"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0020122.g003", "stats"=>{"downloads"=>1, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Analysis_of_Integrase_model_tetramers_and_hetero_octamers_/442410", "title"=>"Analysis of Integrase model tetramers and hetero-octamers.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 18:08:55"}
• {"files"=>["https://ndownloader.figshare.com/files/772824"], "description"=>"<p>*‘del’ indicate that the residue is deleted or was not present in one or more structures.</p>", "links"=>[], "tags"=>["ck2", "sites", "strains"], "article_id"=>443191, "categories"=>["Information And Computing Sciences", "Biological Sciences"], "users"=>["David Sargeant", "Sandeep Deverasetty", "Yang Luo", "Angel Villahoz Baleta", "Stephanie Zobrist", "Viraj Rathnayake", "Jacqueline C. Russo", "Jay Vyas", "Mark A. Muesing", "Martin R. Schiller"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0020122.t001", "stats"=>{"downloads"=>0, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Sequence_conservation_of_CK2_sites_in_different_strains_of_HIV_1_/443191", "title"=>"Sequence conservation of CK2 sites in different strains of HIV-1.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-20 18:13:09"}
• {"files"=>["https://ndownloader.figshare.com/files/772168"], "description"=>"<p>(<b>A</b>) A model of HIV-1 IN complex with 4 IN subunits, 4 LEDGF subunits (light gray), and two viral DNA strands (dark gray); (<b>A, B</b>) Left panels (IN NTD = green, CCD = blue, CTD = red. (<b>A, B</b>) Right panels show functional sites (green = DNA binding), red = dimerization interface in 1EX4 <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0020122#pone.0020122-Chen1\" target=\"_blank\">[10]</a>, cyan = dimerization interface in 1WJA <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0020122#pone.0020122-Cai1\" target=\"_blank\">[11]</a>; blue = tetramerization interface in 1K6Y <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0020122#pone.0020122-Wang1\" target=\"_blank\">[8]</a>; purple = zinc binding site <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0020122#pone.0020122-Cai1\" target=\"_blank\">[11]</a>; brown = reverse transcriptase binding site <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0020122#pone.0020122-Wilkinson1\" target=\"_blank\">[31]</a>, light brown = tetramerization residues <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0020122#pone.0020122-Lutzke2\" target=\"_blank\">[16]</a>. (<b>B</b>) A 90° rotation about the Y-axis of <b>A</b>. Orange arrowhead indicated channel proposed to bind target DNA <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0020122#pone.0020122-Hare1\" target=\"_blank\">[36]</a>.</p>", "links"=>[], "tags"=>["dna", "pfv"], "article_id"=>442532, "categories"=>["Information And Computing Sciences", "Biological Sciences"], "users"=>["David Sargeant", "Sandeep Deverasetty", "Yang Luo", "Angel Villahoz Baleta", "Stephanie Zobrist", "Viraj Rathnayake", "Jacqueline C. Russo", "Jay Vyas", "Mark A. Muesing", "Martin R. Schiller"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0020122.g004", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_model_of_IN_LEDGF_viral_DNA_based_on_the_PFV_IN_structure_/442532", "title"=>"A model of IN:LEDGF:viral DNA based on the PFV IN structure.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 18:09:30"}

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F1000Prime