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Blind and Visually Impaired Students Can Perform Computer-Aided Molecular Design with an Assistive Molecular Fabricator

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Part of the Lecture Notes in Computer Science book series (LNBI,volume 9043)


Life science in general and chemistry in particular are inaccessible to blind and visually impaired (BVI) students at the exception of very few individ-uals who have overcome, in a seemingly miraculous way, the hurdles that pave the way to higher education and professional competency. AsteriX-BVI a publicly accessible web server, developed at the Radboud University in the Netherlands already allows BVI scientists to perform a complete series of tasks to automatically manage results of quantum chemical calculations and produce a 3D representation of the optimized structures into a 3D printable, haptic-enhanced format that includes Braille annotations.1

We report here the implementation of Molecular Fabricator 1.0, a molecular editor which is a new assistive feature of AsteriX-BVI. This molecular editor allows BVI scientists to conceptualize complex organic molecules in their mind and subsequently create them via the server. It was developed around the concept that molecules are composed of chemical fragments connected together. Fragments from either a predefined dictionary or defined as short SMILES strings can be used, ensuring that almost any structure can be generated. A fragment-based relative atom-numbering scheme that can be mentally tracked is used together with the support of an automatically generated report in Braille providing topological information and a clean 2D sketch of the constructed molecule, that can be unambiguously recognized tactilely. The R or S stereo-chemical configuration of asymmetric centers is controlled via feedback provided in the Braille report. The molecular fabricator creates output files in a variety of formats currently used in drug design and theoretical chemistry. It was tested and refined with the help of HBW, the blind co-author of this article, who pursues a PhD in chemistry at UC Davis, California. With Molecular Fab-ricator 1.0 HBW can now create molecules very fast and verify their structures without external help as was the case before. Molecular Fabricator 1.0 and its tutorial are accessible at: .


  • Blind
  • visually impaired
  • chemistry
  • molecular editor
  • assistive software
  • computer-aided molecular design
  • Braille
  • science
  • higher education

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  1. Lounnas V., Wedler H.B., Newman T., Schaftenaar G., Harrison J.G., Nepomuceno G., Pem-berton R., Tantillo D.J., Vriend G.: Visually impaired researchers get their hands on quantum chemistry: application to a computational study on the isomerization of a sterol. J. Comput. Aided Mol. Des. (August 5, 2014) (Epub. ahead of print)

    Google Scholar 

  2. Wedler, H.B., Boyes, L., Davis, R.L., Flynn, D., Franz, A.K., Hamann, C.S., Harrison, J.G., Lodewyk, M.W., Milinkevich, K.R., Shaw, J.T., Tantillo, D.J., Wang, S.C.: Nobody Can See Atoms: Science Camps Highlighting Approaches for Making Chemistry Accessible to Blind and Visually-Impaired Students. J. Chem. Educ. 91, 188–194 (2014)

    CrossRef  Google Scholar 

  3. Albright professor helps blind students discover chemistry at summer camps,

  4. History of Analytical Chemistry by Ferenc Szabadvary, Gordon and Breach Sciences Pub-lishers, Yverdon, Switzerland Horstmann, August (1843 – 1929) studied at the University of Heidelberg, and later became a professor there. He became blind quite young as the re-sult of a disease

    Google Scholar 

  5. Blind students confront chemistry lab,

  6. Which problems would a blind person have when applying for a professorship,

  7. Skawinski, W.J., Busanic, T.J., Ofsievich, A.D., Luzhkov, V.B., Venanzi, T.J., Venanzi, C.A.: The Use of Laser Stereolithography to Produce Three-Dimensional Tactile Molecular Models for Blind and Visually-Impaired Scientists and Students. Inf. Technol. Disabil. 1(4), Article 6 (1994)

    Google Scholar 

  8. Chemistry by touch: blind scientist fashions new models of molecules, (accessed April 30, 2014)

  9. Fartaria, R.P.S., Pereira, F., Bonifácio, V.B.D., Mata, P., Aires-de-Sousa, J., Lobo, A.M.: NavMol 2.0: a molecular structure navigator/editor for blind and visually impaired users. Eur. J. Org. Chem. 1415–1419 (2013)

    Google Scholar 

  10. Lounnas, V., Vriend, G.: AsteriX: A Web Server To Automatically Extract Ligand Coordinates from Figures in PDF Articles. J. Chem. Inf. Model. 52(2), 568–576 (2012), , doi:10.1021/ci2004303

    CrossRef  Google Scholar 

  11. SMILES – A Simplified Chemical Language,

  12. ChemAxon Home Page, (accessed April 30, 2014)

  13. O’Boyle, N.M., Banck, M., James, C.A., Morley, C., Vandermeersch, T., Hutchison, G.R.: Open Babel: An open chemical toolbox. Journal of Cheminformatics 3, 33 (2011), doi:10.1186/1758-2946-3-33

    CrossRef  Google Scholar 

  14. Schaftenaar, G., Noordik, J.H.: Molden: a pre- and post-processing program for mo-lecular and electronic structures. J. Comput-Aided Mol. Design. 14, 123–134 (2000)

    CrossRef  Google Scholar 

  15. Cactvs editor,

  16. Humanware, developers of PIAF, (accessed April 23, 2014)

  17. Antonopoulos, K., Valet, N., Spiratos, D., Siragakis, G.: Olive oil and pomace olive oil processing. Grasas Y Aceites 57, 56–67 (2006)

    Google Scholar 

  18. Wedler, H.B., Pemberton, R.P., Lounnas, V., Vriend, G., Tantillo, D.J., Wang, S.C.: Quantum Chemical Study of the Isomerization of 24-Methylenecycloarta- nol, A Potential Marker of Olive Oil Refining. J. Agric. Food. Chem. (submitted)

    Google Scholar 

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Lounnas, V., Wedler, H.B., Newman, T., Black, J., Vriend, G. (2015). Blind and Visually Impaired Students Can Perform Computer-Aided Molecular Design with an Assistive Molecular Fabricator. In: Ortuño, F., Rojas, I. (eds) Bioinformatics and Biomedical Engineering. IWBBIO 2015. Lecture Notes in Computer Science(), vol 9043. Springer, Cham.

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