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Naview: A d3.js Based JavaScript Library for Drawing and Annotating Voltage-Gated Sodium Channels Membrane Diagrams

Voltage-gated sodium channels (Nav) are membrane proteins essential to initiating and propagating action potential in neurons and other excitable cells. For a given organism there are often multiple, specialized sodium channels found in different tissues, whose mutations can cause deleterious effect...

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Autores principales: Afonso, Marcelo Querino Lima, da Fonseca Júnior, Néli José, Miranda, Thainá Godinho, Bleicher, Lucas
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9580940/
https://www.ncbi.nlm.nih.gov/pubmed/36304314
http://dx.doi.org/10.3389/fbinf.2022.774417
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author Afonso, Marcelo Querino Lima
da Fonseca Júnior, Néli José
Miranda, Thainá Godinho
Bleicher, Lucas
author_facet Afonso, Marcelo Querino Lima
da Fonseca Júnior, Néli José
Miranda, Thainá Godinho
Bleicher, Lucas
author_sort Afonso, Marcelo Querino Lima
collection PubMed
description Voltage-gated sodium channels (Nav) are membrane proteins essential to initiating and propagating action potential in neurons and other excitable cells. For a given organism there are often multiple, specialized sodium channels found in different tissues, whose mutations can cause deleterious effects observed in numerous diseases. Consequently, there is high medical and pharmacological interest in these proteins. Scientific literature often uses membrane diagrams to depict important patterns in these channels including the six transmembrane segments (S1–S6) present in four different homologous domains (D1–D4), the S4 voltage sensors, the pore-lining residue segments and the ion selectivity filter residues, glycosylation and phosphorylation residues, toxin binding sites and the inactivation loop, among others. Most of these diagrams are illustrated either digitally or by hand and programs specifically dedicated to the interactive and data-friendly generation of such visualizations are scarce or non-existing. This paper describes Naview, an open-source javascript visualization compatible with modern web browsers for the dynamic drawing and annotation of voltage-gated sodium channels membrane diagrams based on the D3.js library. By using a graphical user interface and combining user-defined annotations with optional UniProt code as inputs, Naview allows the creation and customization of membrane diagrams. In this interface, a user can also map and display important sodium channel properties, residues, regions and their relationships through symbols, colors, and edge connections. Such features can facilitate data exploration and provide fast, high-quality publication-ready graphics for this highly active area of research.
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spelling pubmed-95809402022-10-26 Naview: A d3.js Based JavaScript Library for Drawing and Annotating Voltage-Gated Sodium Channels Membrane Diagrams Afonso, Marcelo Querino Lima da Fonseca Júnior, Néli José Miranda, Thainá Godinho Bleicher, Lucas Front Bioinform Bioinformatics Voltage-gated sodium channels (Nav) are membrane proteins essential to initiating and propagating action potential in neurons and other excitable cells. For a given organism there are often multiple, specialized sodium channels found in different tissues, whose mutations can cause deleterious effects observed in numerous diseases. Consequently, there is high medical and pharmacological interest in these proteins. Scientific literature often uses membrane diagrams to depict important patterns in these channels including the six transmembrane segments (S1–S6) present in four different homologous domains (D1–D4), the S4 voltage sensors, the pore-lining residue segments and the ion selectivity filter residues, glycosylation and phosphorylation residues, toxin binding sites and the inactivation loop, among others. Most of these diagrams are illustrated either digitally or by hand and programs specifically dedicated to the interactive and data-friendly generation of such visualizations are scarce or non-existing. This paper describes Naview, an open-source javascript visualization compatible with modern web browsers for the dynamic drawing and annotation of voltage-gated sodium channels membrane diagrams based on the D3.js library. By using a graphical user interface and combining user-defined annotations with optional UniProt code as inputs, Naview allows the creation and customization of membrane diagrams. In this interface, a user can also map and display important sodium channel properties, residues, regions and their relationships through symbols, colors, and edge connections. Such features can facilitate data exploration and provide fast, high-quality publication-ready graphics for this highly active area of research. Frontiers Media S.A. 2022-02-11 /pmc/articles/PMC9580940/ /pubmed/36304314 http://dx.doi.org/10.3389/fbinf.2022.774417 Text en Copyright © 2022 Afonso, da Fonseca Júnior, Miranda and Bleicher. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Bioinformatics
Afonso, Marcelo Querino Lima
da Fonseca Júnior, Néli José
Miranda, Thainá Godinho
Bleicher, Lucas
Naview: A d3.js Based JavaScript Library for Drawing and Annotating Voltage-Gated Sodium Channels Membrane Diagrams
title Naview: A d3.js Based JavaScript Library for Drawing and Annotating Voltage-Gated Sodium Channels Membrane Diagrams
title_full Naview: A d3.js Based JavaScript Library for Drawing and Annotating Voltage-Gated Sodium Channels Membrane Diagrams
title_fullStr Naview: A d3.js Based JavaScript Library for Drawing and Annotating Voltage-Gated Sodium Channels Membrane Diagrams
title_full_unstemmed Naview: A d3.js Based JavaScript Library for Drawing and Annotating Voltage-Gated Sodium Channels Membrane Diagrams
title_short Naview: A d3.js Based JavaScript Library for Drawing and Annotating Voltage-Gated Sodium Channels Membrane Diagrams
title_sort naview: a d3.js based javascript library for drawing and annotating voltage-gated sodium channels membrane diagrams
topic Bioinformatics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9580940/
https://www.ncbi.nlm.nih.gov/pubmed/36304314
http://dx.doi.org/10.3389/fbinf.2022.774417
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