2013
DOI: 10.1186/1758-2946-5-6
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Chemical datuments as scientific enablers

Abstract: This article is an attempt to construct a chemical datument as a means of presenting insights into chemical phenomena in a scientific journal. An exploration of the interactions present in a small fragment of duplex Z-DNA and the nature of the catalytic centre of a carbon-dioxide/alkene epoxide alternating co-polymerisation is presented in this datument, with examples of the use of three software tools, one based on Java, the other two using Javascript and HTML5 technologies. The implications for the evolution… Show more

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Cited by 12 publications
(8 citation statements)
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References 21 publications
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“…This places the data associated with this article on an equal footing with the article itself; both have an assigned doi that can be easily used to retrieve the information. In this instance, the repository links are to the Figshare system, which is a modern open-access repository in which all the objects are on unrestricted access . Each item is also duplicated in another repository based on the DSpace system .…”
Section: Introductionmentioning
confidence: 99%
“…This places the data associated with this article on an equal footing with the article itself; both have an assigned doi that can be easily used to retrieve the information. In this instance, the repository links are to the Figshare system, which is a modern open-access repository in which all the objects are on unrestricted access . Each item is also duplicated in another repository based on the DSpace system .…”
Section: Introductionmentioning
confidence: 99%
“…Further, ElliPro suite (Ponomarenko et al ., ) was used for the prediction of linear and conformational B cell epitopes. It implements Thornton's method (Barlow et al ., ) and, together with, the Jmol viewer (Rzepa, ) and MODELLER (Eswar et al ., ) program, allows the prediction and visualization of 3D B cell epitopes in a given protein sequence. It implements three algorithms performing the following tasks: (i) protein shape approximation as an ellipsoid (Kawaji et al ., ); (ii) residue Protrusion Index (PI) calculation (Dupont and Murray, ); and (iii) on the basis of PI values clustering of neighboring residues.…”
Section: Methodsmentioning
confidence: 99%
“…Consider however an alternative model (Figure ). It now incorporates perhaps the single most important game-changing technology introduced a little less than 10 years ago, the digital repository in chemistry and other subject domains. This combines the concept of using rich (reliable) metadata to describe a dataset with an infrastructure that allows automated retrievals of the datasets, potentially on a vast scale. The other basic component of a digital repository is the idea of a persistent identifier for the data, one that can be abstracted away from any explicit hardware installation.…”
Section: The Electronic Notebookmentioning
confidence: 99%