BioFET-SIM Web Interface: Implementation and Two Applications
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{"title"=>"BioFET-SIM Web Interface: Implementation and Two Applications", "type"=>"journal", "authors"=>[{"first_name"=>"Martin R.", "last_name"=>"Hediger", "scopus_author_id"=>"55385421800"}, {"first_name"=>"Jan H.", "last_name"=>"Jensen", "scopus_author_id"=>"7404521532"}, {"first_name"=>"Luca", "last_name"=>"de Vico", "scopus_author_id"=>"6507269968"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-84867301330", "pmid"=>"23056201", "sgr"=>"84867301330", "doi"=>"10.1371/journal.pone.0045379", "isbn"=>"1932-6203", "issn"=>"19326203", "pui"=>"365821692", "arxiv"=>"1204.6140"}, "id"=>"ac3be0dd-bf9f-353f-bdab-32607c183e25", "abstract"=>"We present a web interface for the BioFET-SIM program. The web interface allows to conveniently setup calculations based on the BioFET-SIM multiple charges model. As an illustration, two case studies are presented. In the first case, a generic peptide with opposite charges on both ends is inverted in orientation on a semiconducting nanowire surface leading to a corresponding change in sign of the computed sensitivity of the device. In the second case, the binding of an antibody/antigen complex on the nanowire surface is studied in terms of orientation and analyte/nanowire surface distance. We demonstrate how the BioFET-SIM web interface can aid in the understanding of experimental data and postulate alternative ways of antibody/antigen orientation on the nanowire surface.", "link"=>"http://www.mendeley.com/research/biofetsim-web-interface-implementation-two-applications", "reader_count"=>11, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>2, "Student > Ph. D. Student"=>7, "Student > Bachelor"=>1, "Researcher"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>2, "Student > Ph. D. Student"=>7, "Student > Bachelor"=>1, "Researcher"=>1}, "reader_count_by_subject_area"=>{"Engineering"=>5, "Unspecified"=>1, "Materials Science"=>1, "Physics and Astronomy"=>3, "Immunology and Microbiology"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>5}, "Materials Science"=>{"Materials Science"=>1}, "Physics and Astronomy"=>{"Physics and Astronomy"=>3}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Unspecified"=>{"Unspecified"=>1}}, "group_count"=>0}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/298633", "https://ndownloader.figshare.com/files/298817", "https://ndownloader.figshare.com/files/298873", "https://ndownloader.figshare.com/files/298936", "https://ndownloader.figshare.com/files/298990"], "description"=>"<div><p>We present a web interface which allows us to conveniently set up calculations based on the BioFET-SIM model. With the interface, the signal of a BioFET sensor can be calculated depending on its parameters, as well as the signal dependence on pH. As an illustration, two case studies are presented. In the first case, a generic peptide with opposite charges on both ends is inverted in orientation on a semiconducting nanowire surface leading to a corresponding change in sign of the computed sensitivity of the device. In the second case, the binding of an antibody/antigen complex on the nanowire surface is studied in terms of orientation and analyte/nanowire surface distance. We demonstrate how the BioFET-SIM web interface can aid in the understanding of experimental data and postulate alternative ways of antibody/antigen orientation on the nanowire surface.</p> </div>", "links"=>[], "tags"=>["biofet-sim", "applications"], "article_id"=>118891, "categories"=>["Physics", "Biochemistry", "Biophysics", "Immunology", "Biotechnology", "Chemistry"], "users"=>["Martin R. Hediger", "Jan H. Jensen", "Luca De Vico"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0045379.s001", "https://dx.doi.org/10.1371/journal.pone.0045379.s002", "https://dx.doi.org/10.1371/journal.pone.0045379.s003", "https://dx.doi.org/10.1371/journal.pone.0045379.s004", "https://dx.doi.org/10.1371/journal.pone.0045379.s005"], "stats"=>{"downloads"=>30, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/BioFET_SIM_Web_Interface_Implementation_and_Two_Applications/118891", "title"=>"BioFET-SIM Web Interface: Implementation and Two Applications", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-10-08 02:28:11"}
  • {"files"=>["https://ndownloader.figshare.com/files/562984"], "description"=>"<p>Antigen charge distribution is bound to the right Fab.</p>", "links"=>[], "tags"=>["lying", "nw"], "article_id"=>233476, "categories"=>["Physics", "Biochemistry", "Biophysics", "Immunology", "Biotechnology", "Chemistry"], "users"=>["Martin R. Hediger", "Jan H. Jensen", "Luca De Vico"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0045379.g009", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Antibody_in_orientation_F_lying_on_NW_surface_/233476", "title"=>"Antibody in orientation F lying on NW surface.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-10-08 00:57:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/562597"], "description"=>"<p>Manual rotation of a generic KK{8A}DD peptide in the Jmol applet.</p>", "links"=>[], "tags"=>["rotation", "generic", "peptide", "jmol"], "article_id"=>233094, "categories"=>["Physics", "Biochemistry", "Biophysics", "Immunology", "Biotechnology", "Chemistry"], "users"=>["Martin R. Hediger", "Jan H. Jensen", "Luca De Vico"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0045379.g004", "stats"=>{"downloads"=>3, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Manual_rotation_of_a_generic_KK_8A_DD_peptide_in_the_Jmol_applet_/233094", "title"=>"Manual rotation of a generic KK{8A}DD peptide in the Jmol applet.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-10-08 00:51:34"}
  • {"files"=>["https://ndownloader.figshare.com/files/562885"], "description"=>"<p>A: Binding by C-termini. B: Binding by N-terminus.</p>", "links"=>[], "tags"=>["dependence", "debye"], "article_id"=>233383, "categories"=>["Physics", "Biochemistry", "Biophysics", "Immunology", "Biotechnology", "Chemistry"], "users"=>["Martin R. Hediger", "Jan H. Jensen", "Luca De Vico"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0045379.g008", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Computed_dependence_of_relative_sensitivity_factor_on_Debye_screening_length_/233383", "title"=>"Computed dependence of relative sensitivity factor on Debye screening length.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-10-08 00:56:23"}
  • {"files"=>["https://ndownloader.figshare.com/files/562699"], "description"=>"<p>A: The data series corresponds to either the Asp or Lys residues being close to the nanowire surface in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0045379#pone-0045379-g004\" target=\"_blank\">Figs. 4A and C</a>. The black data series corresponds to both Asp and Lys residues being equally distant from the surface, as in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0045379#pone-0045379-g004\" target=\"_blank\">Fig.4B</a>. B: Dependence of on , <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0045379#pone.0045379.e017\" target=\"_blank\">Eq. 2</a>, for different values of and nm. For nm, the function vanishes for nm.</p>", "links"=>[], "tags"=>["debye", "dependence"], "article_id"=>233193, "categories"=>["Physics", "Biochemistry", "Biophysics", "Immunology", "Biotechnology", "Chemistry"], "users"=>["Martin R. Hediger", "Jan H. Jensen", "Luca De Vico"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0045379.g005", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Dependence_of_sensitivity_on_orientation_and_Debye_length_and_dependence_on_/233193", "title"=>"Dependence of sensitivity on orientation and Debye length and dependence on .", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-10-08 00:53:13"}
  • {"files"=>["https://ndownloader.figshare.com/files/562757"], "description"=>"<p>C-termini in gray at antibody base, N-terminus on Fab in brown.</p>", "links"=>[], "tags"=>["prepared"], "article_id"=>233259, "categories"=>["Physics", "Biochemistry", "Biophysics", "Immunology", "Biotechnology", "Chemistry"], "users"=>["Martin R. Hediger", "Jan H. Jensen", "Luca De Vico"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0045379.g006", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Illustration_of_custom_prepared_antibody_antigen_system_/233259", "title"=>"Illustration of custom prepared antibody/antigen system.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-10-08 00:54:19"}
  • {"files"=>["https://ndownloader.figshare.com/files/563075"], "description"=>"<p>The analytical expression for is given in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0045379#pone.0045379.e039\" target=\"_blank\">Eq. 3</a>.</p>", "links"=>[], "tags"=>["immunology", "chemistry", "biotechnology", "biophysics", "physics", "Biochemistry"], "article_id"=>233565, "categories"=>["Physics", "Biochemistry", "Biophysics", "Immunology", "Biotechnology", "Chemistry"], "users"=>["Martin R. Hediger", "Jan H. Jensen", "Luca De Vico"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0045379.t001", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_BioFET_SIM_parameters_/233565", "title"=>"BioFET-SIM parameters.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-10-08 00:59:25"}
  • {"files"=>["https://ndownloader.figshare.com/files/562835"], "description"=>"<p>The antigen is indicated by a red arc. The antibody base is indicated by a double line. The point of attachement to the NW surface is indicated by the small circle. Orientations A, C, G are bound by the C-termini. Orientations B, D, E, F are bound by the N-terminus.</p>", "links"=>[], "tags"=>["studied", "antibody"], "article_id"=>233328, "categories"=>["Physics", "Biochemistry", "Biophysics", "Immunology", "Biotechnology", "Chemistry"], "users"=>["Martin R. Hediger", "Jan H. Jensen", "Luca De Vico"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0045379.g007", "stats"=>{"downloads"=>1, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Definition_of_studied_antibody_orientations_/233328", "title"=>"Definition of studied antibody orientations.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-10-08 00:55:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/562520"], "description"=>"<p>Red area indicating coverage of the NW by a single biomolecule.</p>", "links"=>[], "tags"=>["occupied"], "article_id"=>233014, "categories"=>["Physics", "Biochemistry", "Biophysics", "Immunology", "Biotechnology", "Chemistry"], "users"=>["Martin R. Hediger", "Jan H. Jensen", "Luca De Vico"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0045379.g003", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Illustration_of_occupied_surface_area_on_NW_/233014", "title"=>"Illustration of occupied surface area on NW.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-10-08 00:50:14"}
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PMC Usage Stats | Further Information

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Relative Metric

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