Literature DB >> 25091066

Visually impaired researchers get their hands on quantum chemistry: application to a computational study on the isomerization of a sterol.

Valère Lounnas1, Henry B Wedler, Timothy Newman, Gijs Schaftenaar, Jason G Harrison, Gabriella Nepomuceno, Ryan Pemberton, Dean J Tantillo, Gert Vriend.   

Abstract

In molecular sciences, articles tend to revolve around 2D representations of 3D molecules, and sighted scientists often resort to 3D virtual reality software to study these molecules in detail. Blind and visually impaired (BVI) molecular scientists have access to a series of audio devices that can help them read the text in articles and work with computers. Reading articles published in this journal, though, is nearly impossible for them because they need to generate mental 3D images of molecules, but the article-reading software cannot do that for them. We have previously designed AsteriX, a web server that fully automatically decomposes articles, detects 2D plots of low molecular weight molecules, removes meta data and annotations from these plots, and converts them into 3D atomic coordinates. AsteriX-BVI goes one step further and converts the 3D representation into a 3D printable, haptic-enhanced format that includes Braille annotations. These Braille-annotated physical 3D models allow BVI scientists to generate a complete mental model of the molecule. AsteriX-BVI uses Molden to convert the meta data of quantum chemistry experiments into BVI friendly formats so that the entire line of scientific information that sighted people take for granted-from published articles, via printed results of computational chemistry experiments, to 3D models-is now available to BVI scientists too. The possibilities offered by AsteriX-BVI are illustrated by a project on the isomerization of a sterol, executed by the blind co-author of this article (HBW).

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Year:  2014        PMID: 25091066     DOI: 10.1007/s10822-014-9782-7

Source DB:  PubMed          Journal:  J Comput Aided Mol Des        ISSN: 0920-654X            Impact factor:   3.686


  7 in total

1.  Molden: a pre- and post-processing program for molecular and electronic structures.

Authors:  G Schaftenaar; J H Noordik
Journal:  J Comput Aided Mol Des       Date:  2000-02       Impact factor: 3.686

2.  AsteriX: a Web server to automatically extract ligand coordinates from figures in PDF articles.

Authors:  V Lounnas; G Vriend
Journal:  J Chem Inf Model       Date:  2012-02-16       Impact factor: 4.956

3.  Chemistry of extra virgin olive oil: adulteration, oxidative stability, and antioxidants.

Authors:  Edwin N Frankel
Journal:  J Agric Food Chem       Date:  2010-05-26       Impact factor: 5.279

4.  Differentiation of refined and virgin edible oils by means of the trans- and cis-phytol isomer distribution.

Authors:  Walter Vetter; Markus Schröder; Katja Lehnert
Journal:  J Agric Food Chem       Date:  2012-06-07       Impact factor: 5.279

5.  The application of stereolithography to the fabrication of accurate molecular models.

Authors:  W J Skawinski; T J Busanic; A D Ofsievich; T J Venanzi; V B Luzhkov; C A Venanzi
Journal:  J Mol Graph       Date:  1995-04

6.  Formation of triterpenoids throughout Olea europaea fruit ontogeny.

Authors:  Naïm Stiti; Saïda Triki; Marie-Andrée Hartmann
Journal:  Lipids       Date:  2007-01-12       Impact factor: 1.880

7.  A mechanistic paradigm for broad-spectrum antivirals that target virus-cell fusion.

Authors:  Frederic Vigant; Jihye Lee; Axel Hollmann; Lukas B Tanner; Zeynep Akyol Ataman; Tatyana Yun; Guanghou Shui; Hector C Aguilar; Dong Zhang; David Meriwether; Gleyder Roman-Sosa; Lindsey R Robinson; Terry L Juelich; Hubert Buczkowski; Sunwen Chou; Miguel A R B Castanho; Mike C Wolf; Jennifer K Smith; Ashley Banyard; Margaret Kielian; Srinivasa Reddy; Markus R Wenk; Matthias Selke; Nuno C Santos; Alexander N Freiberg; Michael E Jung; Benhur Lee
Journal:  PLoS Pathog       Date:  2013-04-18       Impact factor: 6.823

  7 in total
  1 in total

1.  Quantum chemical study of the isomerization of 24-methylenecycloartanol, a potential marker of olive oil refining.

Authors:  Henry B Wedler; Ryan P Pemberton; Valère Lounnas; Gert Vriend; Dean J Tantillo; Selina C Wang
Journal:  J Mol Model       Date:  2015-04-10       Impact factor: 1.810

  1 in total

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