CMBI Radboudumc

Nijmegen, Netherlands

CMBI Radboudumc

Nijmegen, Netherlands
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Lounnas V.,CMBI Radboudumc | Wedler H.B.,University of California at Davis | Newman T.,University of California at Davis | Schaftenaar G.,CMBI Radboudumc | And 5 more authors.
Journal of Computer-Aided Molecular Design | Year: 2014

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). © 2014 Springer International Publishing Switzerland.


Lounnas V.,CMBI Radboudumc | Wedler H.B.,University of California at Davis | Newman T.,University of California at Davis | Black J.,CMBI Radboudumc | Vriend G.,CMBI Radboudumc
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) | Year: 2015

Life science in general and chemistry in particular are inaccessible to blind and visually impaired (BVI) students at the exception of very few individuals 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 Fabricator 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: http://swift.cmbi.ru.nl/bitmapb/access/runit_bvi.html. © Springer International Publishing Switzerland 2015.


Lange J.,Center of Oncology of Poland | Wyrwicz L.S.,Center of Oncology of Poland | Vriend G.,CMBI Radboudumc
Bioinformatics | Year: 2015

Summary: Intrinsically disordered proteins (IDPs) lack tertiary structure and thus differ from globular proteins in terms of their sequence-structure-function relations. IDPs have lower sequence conservation, different types of active sites and a different distribution of functionally important regions, which altogether make their multiple sequence alignment (MSA) difficult. The KMAD MSA software has been written specifically for the alignment and annotation of IDPs. It augments the substitution matrix with knowledge about post-translational modifications, functional domains and short linear motifs. Results: MSAs produced with KMAD describe well-conserved features among IDPs, tend to agree well with biological intuition, and are a good basis for designing new experiments to shed light on this large, understudied class of proteins. Availability and implementation: KMAD web server is accessible at http://www.cmbi.ru.nl/kmad/. A standalone version is freely available. Contact: © 2015 The Author 2015. Published by Oxford University Press.


PubMed | CMBI Radboudumc and Center of Oncology of Poland
Type: Journal Article | Journal: Bioinformatics (Oxford, England) | Year: 2016

Intrinsically disordered proteins (IDPs) lack tertiary structure and thus differ from globular proteins in terms of their sequence-structure-function relations. IDPs have lower sequence conservation, different types of active sites and a different distribution of functionally important regions, which altogether make their multiple sequence alignment (MSA) difficult. The KMAD MSA software has been written specifically for the alignment and annotation of IDPs. It augments the substitution matrix with knowledge about post-translational modifications, functional domains and short linear motifs.MSAs produced with KMAD describe well-conserved features among IDPs, tend to agree well with biological intuition, and are a good basis for designing new experiments to shed light on this large, understudied class of proteins.KMAD web server is accessible at http://www.cmbi.ru.nl/kmad/ A standalone version is freely available.vriend@cmbi.ru.nl.

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