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Volume 2 Supplement 1

5th German Conference on Cheminformatics: 23. CIC-Workshop

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Progress on an open source computer-assisted structure elucidation suite (SENECA)

Journal of Cheminformatics volume 2, Article number: P34 (2010) Cite this article

We suggested and developed various components for Computer-Assisted Structure Elucidation (CASE) over the years [1, 2]. Our current goal is to integrate these into an easy to use and efficient platform for end users, called SENECA. This is based on Bioclipse [3], an integrated software suite for chemo- and bioinformatics providing plugins for file handling and visualisation of compounds and spectra.

The SENECA feature currently comprises the following components and algorithms:

• A deterministic structure generator suitable for small chemical spaces.

• Simulated Annealing and Genetic Algorithm for random structure walks in large spaces.

Simulation of 13C NMR spectra for ranking results.

SENECA is a Bioclipse feature, available via the update site at http://www.ebi.ac.uk/steinbeck-srv/speclipse/net.bioclipse.seneca-updatesite/.

References

  1. Steinbeck C, Krause S, Kuhn S: NMRShiftDB - Constructing a free chemical information system with open-source components. Journal of Chemical Information and Computer Sciences. 2003, 43: 1733-1739.

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  2. Kuhn S, Egert B, Neumann S, Steinbeck C: Building blocks for automated elucidation of metabolites: Machine learning methods for NMR prediction. BMC Bioinformatics. 2008, 9: 400-. 10.1186/1471-2105-9-400.

    Article  Google Scholar 

  3. Spjuth O, Helmus T, Willighagen EL, Kuhn S, Eklund M, et al: Bioclipse: An open source workbench for chemo- and bioinformatics. BMC Bioinformatics. 2007, 8: 59-10.1186/1471-2105-8-59.

    Article  Google Scholar 

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Authors and Affiliations

  1. Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK

    Stefan Kuhn & Christoph Steinbeck

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  1. Stefan Kuhn
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  2. Christoph Steinbeck
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Open Access This is an open access article distributed under the terms of the Creative Commons Attribution Noncommercial License ( https://creativecommons.org/licenses/by-nc/2.0 ), which permits any noncommercial use, distribution, and reproduction in any medium, provided the original author(s) and source are credited.

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Kuhn, S., Steinbeck, C. Progress on an open source computer-assisted structure elucidation suite (SENECA). J Cheminform 2 (Suppl 1), P34 (2010). https://doi.org/10.1186/1758-2946-2-S1-P34

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  • DOI: https://doi.org/10.1186/1758-2946-2-S1-P34

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Journal of Cheminformatics

ISSN: 1758-2946

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